cephalexin

I’m going to echo what BabyScientist said above. I am PharmD to PhD, and I have never been happier than in my program.
Best aspect: doing what you love all day. When I was in pharmacy school, I spent my free time in a research lab, but I always had to worry about exams, rotations, etc. 
 
worst aspect: money. See Baby’s post. Also not being eligible to apply for some grad student fellowships because of your degree.
 
please let me know if you have any questions about the application process if you decide to apply or if you’d like any other advice, I’m happy to chat/help. With a professional degree, your application will be unique compared to other applicants. I found the whole application-interview process exciting and encouraging, and I am happy to talk about it.

Overall, I think your application is okay, and it really is only lacking in research experience. It seems to me that you only have ~1 semester’s worth of research experience, which is far less than most applicants in science.

Yes. Funding is provided. See https://compneuro.cmu.edu/application-process/

Congratulations!

I used a combination of NextStep and Kaplan books, and I bought a NextStep self-paced course. My MCAT score was trash (498), but I also focused more on my GPA than my MCAT score.
For NexStep I would recommend the 108 CARS Passages book. It's great CARS Practice with explanations for every question. They also have one for discrete questions that was okay. However, there content books seemed to be a little wishy-washy on some material. Like one book would say one thing about a topic but a separate book would say the opposite on the same topic. But other than that their content goes pretty in depth in my opinion.
For Kaplan, I used an older version of just an MCAT Prep set. I though their information was a great overview of everything, just not quite as in depth as NextStep.
For the prep course I bought, you get 10 practice tests through NextStep plus an additional 3 through AAMC. You also get the standard AAMC prep materials (Q-banks, practice tests, etc.) which I though was really helpful. You also get a bunch of NextStep q-banks and whatnot. You build the course according to you schedule. I would trust the NextStep exams. All of mine (roughly 8ish) that I took with NextStep were similar to what I got with my AAMC (all 3) ones and my actual MCAT was about where I expected based on those. There are videos of literally every topic that you can access at any time and they give pretty good explanations. Personally, I think that if you really commit to sticking to the course and doing every single thing they tell you, you can get a great score. I just didn't do that. I put off my studying and tried to mostly study on my own. 

I don't see it hurting, but I doubt they would really look at it unless it was in their field and they were interested. 

I'm SLP to PhD and don't really know the PT field, but: completing the clinical degree and certification may be a definite asset throughout a PhD program and in the faculty job search. Having patient care experience gives you more insight into the public health impact of your research than someone who went straight through school. This will improve your ability to form research questions, justify the significance of those questions to funding agencies (i.e., NIH), and contextualize outcomes in ways that matter to the public. It may also be the case that available faculty positions are in clinical departments, and the ability to teach in the classroom using case examples from your own practice, or to provide clinical supervision, will be a huge selling point for you. I transitioned from social science undergrad and clinical master's degree to a biology lab, and it's been such a huge benefit for my learning to be the person in the room with the least knowledge of cell biology or whatever, but the only person who has ever treated a patient. I get to learn from people with all kinds of expertise, and provide my own unique expertise. It WAS hard psychologically and emotionally to go back to being a student after being a professional, but it was worth it and the coursework period is ultimately so brief. Three years in, I feel like a professional again: I'm done with classes, done with prelims (no more exams ever),  I'm starting to teach, and I've gotten a grant and am working along on a ton of research projects. 
The best aspect is that I get to do research in an area that's really understudied, pursue my ideas, form new collaborations, and carve out my own niche. Patient care is fun, but research is more interesting. Even surgeons say there's a 5-10 year window before you master everything, get bored, and start looking for more intellectual stimulation and get into research anyway. The worst aspect is definitely money, but that's temporary. SLP/CSD is a field that needs PhD-level faculty and I've been told that jobs will be plentiful and ultimately pay more than working as a clinician. We'll see how that plays out. Not sure about PT, though.

It sounds like you'd be a solid applicant for PhD programs and would have a unique perspective.
I've enjoyed my experience thus far. I love research, and it's what I get to do.
Best aspect: Freedom. I guess this depends on your mentor but mine is very open to my ideas and I, with guidance, mostly make my own decisions. My day is dictated by what I want.
Worst aspect: Frankly, you'd make a lot more as a PT. The PhD stipend is, on average, around $30k a year. So you're making around that much for 5-6 years, then if you do a postdoc you make maybe $40-50k a year for the 3-5 years of that. Unless you want to go into industry, then you could make a lot more after your PhD.
That being said, I love what I do and am not doing it for the money. If you truly hate what you're doing, and enjoy the research you're doing, it sounds like a great idea to apply for PhD programs. And I admire your commitment to finish what you've started. Good luck!

@cephalexin 
Thanks so much for replying. This gave me some more schools to look into and hopefully start to concise my list a little more.
I am more interested in research than patient care and am okay with just doing a PhD for now. I'm still interested in doing an MD as well, but I don't mind taking the scenic route and spending a few extra years in school. I'm not opposed to retaking the MCAT, I just don't feel that my score would improve enough right now. If the time comes, I know I'll probably have to pay for med school myself, but I figured if I still wanted to do it bad enough, I'd find a way. 
Thanks again for your help!

Respectfully, absolutely do not take this advice. I am an MD that is now in a PhD program. If you are even questioning whether you like clinical medicine in your first year of medical school, then it is absolutely not for you. Every conversation I have with doctors my age is about our "Out from clinical medicine". I can count on one hand how many physicians I know that do not regret going to medical school.
In more detail:
1) I did research in undergrad and between MS1 and MS2 years. This is enough time to get a good publication out, but not to develop real research independence. The problem with medical school is that every step along the way in clinical training is a complete stop in research momentum. Imaging a PI having to restart his/her career every 4 years. That is what medical school, residency, clinical fellowship, etc do to you.
2) Entering a PhD program after med school (as I did) is not wise unless you enjoy 300k of student loan debt. Also, the pool of successful research scientists that are MD-only and have research skill gained from research fellowships post clinical training is shrinking. Many grants that apply to work in anything other than very basic clinical research want the PhD. 10-20 years ago this was not the case, but it is now. Compound that with the burden of clinical/teaching/admin duties as an MD and you get the point.
4) There is truth here, but the job market for PhDs, especially in industry, where a lot of interesting research now occurs, is hot.
Take the advice or leave it. There is a reason that almost 20% of doctors are planning to leave clinical medicine: https://www.beckershospitalreview.com/hospital-physician-relationships/why-more-physicians-are-leaving-medicine-4-takeaways.html. I would guess that number from 2016 is closer to 25-30% now.

pharmCAS provides information about some (but not all) graduate programs in pharmaceutical science (including med chem and pharmacology), including recommended GRE scores. That might be a good place to start. However, not all programs use pharmCAS, and so you may also want to look at American Association of Colleges of Pharmacy's website.

I’m going to mostly agree with what eevee said above. The only thing I would add is to try and network at your institution. You say you’re in your desired field so does anyone in your lab or a lab in your department know anyone at programs your interested in? It is never too early to start looking at programs and their respective faculty and seeing what catches your eye.

To add to the discussion on iPads, I use an iPad mini, and I love it. I originally went with the mini because of price but honestly prefer the smaller size. I also use a generic metal mesh stylus  (brand: the friendly Swede) and notability as my app of choice. It works great for importing papers and annotating them.

A couple reasons come to mind immediately:
1) Schools with more prestige have more money and can support their graduate students better. Better-supported graduate students do better scholarship. 
2) Students at prestigious schools encounter a greater number of prestigious professors, and therefor have better models of how to perform academic intelligence. 
3) Name recognition matters on applications - prestigious schools offer a way to winnow a 100 person application file because the people they produce are, within reason, known quantities.

This is a great start. Congrats!

Your best bet right now is probably being direct. Ask if she will write you a positive letter, and make sure you specific “positive.”

1) Communicating your research. Is there a possibility for you to work on a paper? Not necessarily first authorship or anything, but is there anyone in the lab working on something related to your work for which you could help develop a figure or two, do some analysis, or help write up a lit review and maybe get a second or third author position? Alternatively, even though you said there are no relevant conferences coming up in the next 2 months, look at ones that are coming up later and submit an abstract / work on a poster for those. While larger conferences are better for networking, you could also look for a smaller, local, or even just university-specific one. For example, my college had undergrad research symposium just for undergrads to present their work.
2) As you're compiling your list of programs, start reaching out to faculty you might be interested in working with and/or students in the programs, and see if you can set up short skype/phone informational interviews. It's low stress but a good way to both learn more about the program and also show that you're a committed applicant. 
Best of luck!! 

This may have been almost true - or at least you could plausibly argue it - 10 years ago; it is no longer. That middle tier of "undergrad" institution is rapidly collapsing, and what jobs do exist are being hotly contested by grads from Harvard, Yale, Chicago, and the like. I know plenty of Ivy graduates, and they are universally thrilled if they manage to land a permanent position at a branch campus or community college. That's the brutal reality of the current market.
Sure. If you're at a prestigious institution, you get Important Scholars swinging by weekly to give a talk, because prestige and money go hand in hand. Guess who has the advantage there.
Me too, and mostly they are. It doesn't mean that they're unimportant, though, and school rank corresponds to many structural advantages such as (as I have already said) increased visibility to important scholars, extra funding, and lighter teaching loads, all of which enable higher-quality research.
Alas that the world is the way it is, and not the way you want it to be.
Again, this may have been true when that professor was on the market however many decades ago, but this is absolute nonsense today. I can give you lists of absolutely brilliant friends from really good institutions who simply have been unlucky in the preferences of the hiring committee or have only had 3 (!!) job listings in their subfields, and are now adjuncting to make ends meet. Don't trust anyone who's gotten their job before 2014 when it comes to the job market.
If you go into academia thinking it will all work out if you try hard enough, or that you're smarter and are going to do it better than everyone else, you will end up broken, poor, and disappointed. Optimism in this regard is, quite frankly, self-delusion. That's not an opinion. That's simply an observation of reality.

Yeah I agree with this as well. My undergrad was a relatively small unknown college and my PI there said that grad students from our department had gotten academia positions; they just had to work extremely hard for them. 

Agreed.
Also, I don't think this should be a deterrent for the OP to not apply to professorships in the future. Networking is also really important in my mind. Ranking is important, but that's because we view it as important. I think the person's abilities of conducting research and/or teaching a class should be more important than the rank of the school they went to. The school could have a bad-ish rank, but that doesn't meant that the skills they learned in schools aren't good, especially in grad school because what you learn during that time is dependent on various things, such as your PI, conferences you attend, groups, organizations, and societies you join, how well you write research articles/grants/proposals, etc. Sometimes those things are dependent on the program and other things are dependent on the student and their PI. I believe ranking shouldn't be so heavily used in determining if you would be a good professor or not. Just my opinion.