psstein

Not profoundly.  You're just getting the experience.
The most important thing is to focus on your writing sample and clarifying the questions you'd like to explore as a PhD student. I also would keep working on languages (or start on something related to your area of interest).  Finally, understand that there is no "reach/match/safety" in PhD admissions.  As with academia as a whole, much also depends on luck.  I also encourage you to look beyond the East Coast as being part of academia does require one to be mobile as possible, particularly if one is interested in a tenure-track professor job at the end.

Either go to a top-tier program or don't go at all is my advice.
UVA, Baylor, Emory, and to a lesser extent, Notre Dame, do not place people exceptionally well. Yale and Chicago, of course, have very good placement and more resources than you can shake a stick at.

To answer your question, I don't really know. It sounds like your major deficiencies may be in language preparation. I wouldn't be so worried about how long it took to do your BA in history.
Honestly, I would consider waiting a year or two before starting the MA. You may find that you like your job enough that you don't want the MA or PhD.

To answer your question, I don't really know. It sounds like your major deficiencies may be in language preparation. I wouldn't be so worried about how long it took to do your BA in history.
Honestly, I would consider waiting a year or two before starting the MA. You may find that you like your job enough that you don't want the MA or PhD.

I can't say I agree with you here. The history of science/tech/medicine market has always been very small and not particularly robust. History of science is kind of in a liminal position right now. There's been an ongoing trend towards history of science departments/programs consolidating into history programs, which is not good in the long term for history of science.
Certain areas of history of science are particularly trendy right now, but the field as a whole is much less so.

Don't overwhelm yourself with languages.  Stay focused on your Latin until you can read the primary sources more comfortably with some dictionary help. Unless you're really one of those super talented linguists, trying to learn multiple new languages and keeping them straight is difficult enough as it is for the brain.  Once you have Latin down, French will come more easily so put away your French materials.

If you sustain this interest in disease, I hope you have the chance to take medical sociology/anthropology of medicine courses. These classes were much more helpful for my thinking about disease and medicine issues than my history of medicine courses. The contemporary focus may seem remote, but many sociologists and anthropologists are very interested in plural conceptions of disease and the body, so it might be more useful than you would assume.

Studii fuit apud ueteribus et eruditissimis uiris ut eorum quorum miracula sanctis actibus pollere cernebant sagaci studio Christo auspice sine quo nihil boni agitur stilo promulgarent quatinus de praecedentium meritis imitando uel memoriae commendando uentura sobolis gloriaretur
 
 
(It was a thing of passion among old and most learned men, that they should make known by the pen those among them, the miracles of whom they discerned with keen insight and by Christ’s help (without whom nothing good may come to pass) to be strong in holiness, since future generations might win themselves glory by imitating the good works of their ancestors and by being entrusted with their memory.)
Just FYI.

Yeah, this was my approach as well. I rarely take notes during a class, unless it's some particularly insightful point someone made or I want to say something down the road.
@historygeek, I'd recommend reading with a heuristic tool called IPSO. It stands for Issue, Position, Support, and Outcome. I stole it from my friend, who uses it for reading/teaching. It's very useful for teaching undergrads how to break down a piece of dense writing into its constituent parts. It works like this?
Issue: What is the research question? What is the author examining?
Position: What is his/her argument or thesis statement?
Support: What evidence does the author use to support the thesis? This includes not only data points, but secondary source scaffolding.
Outcome: So what? If we accept the author's argument, what are the other avenues for research?
I do realize that this framework seems a bit reductive and simplistic, but trust me, it's really helpful when you're reading scholarship that submerges the ideas. In my own field, it's helped me demystify Latour and Simon Schaffer.

Yeah, this was my approach as well. I rarely take notes during a class, unless it's some particularly insightful point someone made or I want to say something down the road.
@historygeek, I'd recommend reading with a heuristic tool called IPSO. It stands for Issue, Position, Support, and Outcome. I stole it from my friend, who uses it for reading/teaching. It's very useful for teaching undergrads how to break down a piece of dense writing into its constituent parts. It works like this?
Issue: What is the research question? What is the author examining?
Position: What is his/her argument or thesis statement?
Support: What evidence does the author use to support the thesis? This includes not only data points, but secondary source scaffolding.
Outcome: So what? If we accept the author's argument, what are the other avenues for research?
I do realize that this framework seems a bit reductive and simplistic, but trust me, it's really helpful when you're reading scholarship that submerges the ideas. In my own field, it's helped me demystify Latour and Simon Schaffer.

Yeah, this was my approach as well. I rarely take notes during a class, unless it's some particularly insightful point someone made or I want to say something down the road.
@historygeek, I'd recommend reading with a heuristic tool called IPSO. It stands for Issue, Position, Support, and Outcome. I stole it from my friend, who uses it for reading/teaching. It's very useful for teaching undergrads how to break down a piece of dense writing into its constituent parts. It works like this?
Issue: What is the research question? What is the author examining?
Position: What is his/her argument or thesis statement?
Support: What evidence does the author use to support the thesis? This includes not only data points, but secondary source scaffolding.
Outcome: So what? If we accept the author's argument, what are the other avenues for research?
I do realize that this framework seems a bit reductive and simplistic, but trust me, it's really helpful when you're reading scholarship that submerges the ideas. In my own field, it's helped me demystify Latour and Simon Schaffer.

Yeah, this was my approach as well. I rarely take notes during a class, unless it's some particularly insightful point someone made or I want to say something down the road.
@historygeek, I'd recommend reading with a heuristic tool called IPSO. It stands for Issue, Position, Support, and Outcome. I stole it from my friend, who uses it for reading/teaching. It's very useful for teaching undergrads how to break down a piece of dense writing into its constituent parts. It works like this?
Issue: What is the research question? What is the author examining?
Position: What is his/her argument or thesis statement?
Support: What evidence does the author use to support the thesis? This includes not only data points, but secondary source scaffolding.
Outcome: So what? If we accept the author's argument, what are the other avenues for research?
I do realize that this framework seems a bit reductive and simplistic, but trust me, it's really helpful when you're reading scholarship that submerges the ideas. In my own field, it's helped me demystify Latour and Simon Schaffer.

I don't. There's no point to them. There aren't any exams except quals, and those are their own separate thing (for these, I did 500-1000 word precis of each item), and in-class notes have no utility for any papers. I did have a notebook I'd write in for class, but that's because it's a way I think through a problem, not for later reference.

Until you try Merovingian Latin, you are yet still a sweet summer child ☠️

May I suggest Villanova? I'm going to be specializing in Medieval history and am doing the European history concentration in their Masters program this fall. I received a full tuition scholarship and a graduate assistant position in their Center for Research and Fellowships.

Toronto has an intensive Medieval Latin program, but I know very little about it beyond that. You're probably a bit better off learning classical Latin and then moving to Medieval rather than the other way around... many Renaissance texts eschew Medieval Latin and attempt to classicize their Latin. As you can probably imagine, this happened with varying degrees of success. Some texts read like Cicero, while others are much more like reading a very badly jumbled maze.
As for honing your early modern interests, there's a lot of great global early modern work. Again, my own bias is coming through here, but Cook's Matters of Exchange is a great read.

@telkanuru is on the mark, as usual. I would probably add CUA into your list, as I said elsewhere. I believe they have a good medieval history program, as well as some funded MA places. I, too, would counsel avoiding Columbia.
I slightly disagree with him as to Latin. It depends what you're working on and how easily you acquire languages, but it's not impossible to do something worthwhile with less Latin than you may think. That being said, my knowledge comes largely from working on medieval astronomy, which has a pretty limited vocabulary. Most historians of science who "know Latin" know it well enough to muddle through it with a dictionary and a grammar. I imagine that it's a bit different for dedicated medievalists.

The more seasoned posters here are probably tired of me banging on about languages for medievalists, but let's start there. Any PhD program of quality - and there's no reason to attend a PhD program which is not quality - will be looking for two modern research languages, typically French and German, in addition to Latin. They will have an abundance of candidates who meet this criteria. Exceptions to this rule usually come if an applicant has very good Latin but no French (everyone thinks French is very easy to acquire quickly), or if they have mastery of an unusual language (Greek, Arabic, Old Church Slavonic, whatever). 
These requirements exist for a very good reason: they are a starting place, and you will usually find you need to learn more languages as you continue your studies. Since my admission, I've picked up reading fluency in Spanish, Dutch, and Italian, for example. Without these skills, you can't get your head around the literature you need or do good work, nor can you work with primary sources. And that's why the requirements mark a program of quality - those who do not have the requirement are taking students who are not well-prepared to succeed. 
I say all this to highlight the point that language acquisition must be your primary goal before you apply to PhD programs, and that you should feel that you need to acquire not only Latin, but also German. Further, Latin is hard for most people to master. Even with 2 years of Latin in your MA, you will probably have to continue working on it as you go for your PhD. Finally, if you're still in the early stages of acquiring Latin, you can't really use it to work with primary sources, meaning you will have a weak writing sample. Consequently, I would advise that you take a year (or even two!) before you apply to MA programs working in the world and picking up the skills you need.
To your specific question on which MA programs, UCBoulder, Fordham, UChicago MAPSS, and St. Andrews are good programs, and I know a lot of people who have graduated from them to continue on to PhD programs. I don't have a fantastic opinion of WMU's program, but it's not the worst. Avoid Columbia.
I would add the following programs: UCLA (I think this still exists), Oxford, Cambridge, Harvard Divinity, Yale/Yale Div. 

They're full of shit. People in grad school are always posturing about how hard they work, but that's all it is. They've got some screwed up idea of what the perfect grad student is, and they constantly fail to meet it, and it wreaks havoc with their brain chemistry. 
Being a good student really isn't inconsistent with maintaining a healthy work-life balance. I was a great grad student: I published two papers in top specialist journals, presented at dozens of conferences, won awards, networked like hell, audited all kinds of classes, TAed every semester, applied for hundreds of jobs, etc. It didn't require me to give up on any hobbies or other fun stuff. And I'm not at all exceptional in that respect. Take the time to do your own thing. It'll help enormously with all the negative crap. Just don't let yourself get too distracted from your end goal!
As for making time for reading, I do most of mine on public transit, or for about an hour in bed at night. I often read during the day, too, but that's mostly down to how I feel in the moment. 
One word of advice: breaking your tasks down into smaller chunks and spreading them over time is way more effective than putting in whole days at a time. Read just one article a day, and by the end of a month that's a whole course's worth of reading; write an hour a day, and after a year you've got a draft of a dissertation, or after a few weeks, you've got a paper to send to conferences and journals; and so on.
The trick is to be consistent, and not to overload yourself with just one task. I try to write for about an hour a day (some days I get excited and it's more, and some days I lose the thread, but on the whole that's pretty much what it averages out to). I do that relatively early in the day, and then it doesn't matter what else I do that day; the pressure's off. I can take an hour or so to read a paper, too, and then that's two big things down. After that, the rest of the day is boring admin work, emails, course prep, whatever. And fun stuff.

Honestly, I think that the most important thing you can do is start professionalizing yourself, especially if you're starting a PhD. Everything else will come during the course of the PhD itself.
So, for example, start familiarizing yourself with the best journals in your subfield, and with the top generalist journals, and what kind of work gets published in which journal. Start developing a sense of how fast the turnaround is in various journals (the Cullison/APA list is helpful for that). Create an account on PhilPapers, and sign up for conference and publication alerts. Start looking at the CVs of grad students, postdocs, and assistant professors at a wide range of departments. In particular, look for people working in your inteded AOSes. Get a sense of what they're doing, and how it seems to have worked out for them. Figure out what the important conferences and associations are in your subfields. Start following the gossip on the main philosophy blogs. Start reading through the Job Market Boot Camp on the Philosophers' Cocoon. Start paying attention to what goes on in the forum over at the Chronicle of Higher Education.
That sort of thing.

No, that really helps. You might do really well in a history/phil. of science program (e.g. Pittsburgh, who have faculty who love this sort of work). Your proposed project sounds absolutely fascinating to me, as historians of science have usually assumed that Galileo's world system finally killed Aristotelianism. There's a lot of good literature to this end, most of which is tied to the Sci. Rev. one way or another. Even of the questions you've put forward, I'd encourage an even narrower dive into one, as well as situating yourself within the literature. I'm happy to point you towards works on the history and phil. of science side.
There are also, generally speaking, ways to learn how to read Latin without MA coursework. I'd also point out that many, if not most early modernists, aren't talented Latin scholars. Most know enough Latin to muddle through sources with a dictionary and a grammar. If you're self-motivated, there are some great self study aids out there, and not just the rather dry Wheelock's Latin.

No, that really helps. You might do really well in a history/phil. of science program (e.g. Pittsburgh, who have faculty who love this sort of work). Your proposed project sounds absolutely fascinating to me, as historians of science have usually assumed that Galileo's world system finally killed Aristotelianism. There's a lot of good literature to this end, most of which is tied to the Sci. Rev. one way or another. Even of the questions you've put forward, I'd encourage an even narrower dive into one, as well as situating yourself within the literature. I'm happy to point you towards works on the history and phil. of science side.
There are also, generally speaking, ways to learn how to read Latin without MA coursework. I'd also point out that many, if not most early modernists, aren't talented Latin scholars. Most know enough Latin to muddle through sources with a dictionary and a grammar. If you're self-motivated, there are some great self study aids out there, and not just the rather dry Wheelock's Latin.

FWIW, my anecdotal impression (from my acquaintances in history) is also that the job market there is better than in philosophy, though still terrible. Think along the lines of 100-200 applicants per job, vs. 300-600.
Also, as everyone else has said, avoid Chicago's cash cows.
It's totally possible to transition into philosophy from outside. It's not even all that hard, in the sense that loads of people do it. While a Master's degree in philosophy would certainly help, the most important thing is to make sure that your writing sample is up to snuff, and clearly philosophical. After that, work hard on your statement of interest, and on explaining why you want to move into philosophy. Clear and distinct (!) reasons are better than generalities, here: you need to make the case that you're serious about philosophy, and that it's the best disciplinary fit for you.
All that said, it's worth reiterating that although the history of philosophy job market is much better than the market for most other general areas, it varies a lot by historical subfield. And scholastic/medieval's job market is terribad. On the order of 1-2 jobs a year (almost always at Catholic institutions). And although there are lots more open/open jobs, they don't often seem to go to scholars working in that time period.

Just on a pure job market level, history's job market is better than philosophy's. I too, find intellectual history fascinating, which sort of puts us both in a tough situation. As you no doubt know, many scholars look at intellectual history with moderate suspicion. They suspect it's a way to disproportionately focus on dead European males, while Pocock and others have shown multiple ways forward. 
My own irritation aside, a few questions: what specifically interests you about Scholastic metaphysics? What research question would you try to answer in a dissertation, and what would your methodology be? If you're asking a historical question like "what intellectual currents caused Anscombe to meld Thomist thought with Wittgenstein's thought?" then you should be in a history department. 
Getting a minor, and developing a top quality philosophy writing sample would almost certainly help your case. 
I wouldn't go for the MAPSS. It's not cheap, and unless you've serious gaps in your preparation (e.g. you need to know Latin, but don't), a terminal MA isn't tremendously useful. 

Just on a pure job market level, history's job market is better than philosophy's. I too, find intellectual history fascinating, which sort of puts us both in a tough situation. As you no doubt know, many scholars look at intellectual history with moderate suspicion. They suspect it's a way to disproportionately focus on dead European males, while Pocock and others have shown multiple ways forward. 
My own irritation aside, a few questions: what specifically interests you about Scholastic metaphysics? What research question would you try to answer in a dissertation, and what would your methodology be? If you're asking a historical question like "what intellectual currents caused Anscombe to meld Thomist thought with Wittgenstein's thought?" then you should be in a history department. 
Getting a minor, and developing a top quality philosophy writing sample would almost certainly help your case. 
I wouldn't go for the MAPSS. It's not cheap, and unless you've serious gaps in your preparation (e.g. you need to know Latin, but don't), a terminal MA isn't tremendously useful.