GeoDUDE!

Your sidebar says your program is Oceanography. I don't think upper level E&M and classical mechanics classes will really matter to Oceanography graduate programs. 
However, even if you are also applying to Physics PhD programs (where these courses would matter), your transcript may show future classes you are registered for or currently taking (just without a grade). This is enough to show that you are enrolled. In addition, most Physics programs I applied to also asked you about courses you plan to take but do not yet show up on the transcript. 
If you are not applying to Physics programs, then you shouldn't even worry about this at all. If you are applying to Physics programs, and neither of the two above options apply, then you can just mention that you are taking these 2 courses in 1 sentence in your SOP. 

that sounds so good.....

close means being able to express these things to your advisor. If you have fear of doing this, you are not close.

You are always going to get harsh reviews, especially from students who think they deserve a higher grade.  It would be one thing if you got mostly average and bad reviews, but from the sound of it, you got a nice gaussian distribution. Forget about it and move on. 

You should submit all transcripts that you are asked to submit. Sometimes, a school will only ask for transcripts from institutions where you completed a degree program. I'm not sure there is much more you can do other than let the school know you are retaking the courses. Hopefully, the program in Geology/Geoscience will not weigh your physics/calculus courses that much so it will have little effect. If you don't get in this year, then perhaps trying again next year with improved grades might help.

Lectures, workshops ect always have free food. Also, anytime you are helping out with something you tend to get food. Also, like at least in my town, they have a bunch of apartment recruitment things where they have like pizza to meet new roommates, and sometimes I go even though I'm not looking for an apartment. Yes, you might say thats unethical, but, they almost always order more food than needed, so its not being wasteful. 

I dont know the situation, but If the TA was cute (and yes, being a women is required to be cute in this case) I would rather speak to her than the dude. But I'm guessing that kinda gender bias is more acceptable? 

You are always going to get harsh reviews, especially from students who think they deserve a higher grade.  It would be one thing if you got mostly average and bad reviews, but from the sound of it, you got a nice gaussian distribution. Forget about it and move on. 

In my opinion, you aren't going to be able to hide your GRE scores. They are either going to be too low or they won't matter enough to sink your application if its strong enough. 
You should be writing about the research you want to do in your statement of purpose, and not about the past.  Listing tutoring, qualifications ect will be on your CV. Why waste space? 
You need to show why what you want to do in the future fits well with what the department wants to do in the future: there are very few applicants (in general) who can eloquently describe that. It is much harder to do that than get a perfect GRE or high GPA. If you are below the cutoffs, nothing you do will matter anyway.

In my opinion, you aren't going to be able to hide your GRE scores. They are either going to be too low or they won't matter enough to sink your application if its strong enough. 
You should be writing about the research you want to do in your statement of purpose, and not about the past.  Listing tutoring, qualifications ect will be on your CV. Why waste space? 
You need to show why what you want to do in the future fits well with what the department wants to do in the future: there are very few applicants (in general) who can eloquently describe that. It is much harder to do that than get a perfect GRE or high GPA. If you are below the cutoffs, nothing you do will matter anyway.

In my opinion, you aren't going to be able to hide your GRE scores. They are either going to be too low or they won't matter enough to sink your application if its strong enough. 
You should be writing about the research you want to do in your statement of purpose, and not about the past.  Listing tutoring, qualifications ect will be on your CV. Why waste space? 
You need to show why what you want to do in the future fits well with what the department wants to do in the future: there are very few applicants (in general) who can eloquently describe that. It is much harder to do that than get a perfect GRE or high GPA. If you are below the cutoffs, nothing you do will matter anyway.

I don't think its good to think that just because one situation is shitty another place should also be shitty. That is essentially your argument, in case you want to revise. 

You haven't taken trig and you want to get an MS in statistics?
 
What makes you think you can even handle a MS in stats let alone do one during a PhD ? 
 
What does doing an MS get you that self learning doesn't ?
 
What you call advanced math most people take in High School (if you consider trig and calc 1 and intro statistics advanced). 
 
Wouldn't you be better spent developing and working on your dissertation? 
 
These are  some questions/comment you should be answering and thinking about

OK, despite rather liking/admiring Kelsky myself (she's been invited to speak at my institution twice), I laughed at that.
 
This is good to know. I did not admit in my post that I revert to backpack on days I bike to campus (something I started doing only recently). But for conferences/job talks, I really make the effort to pare down to a messenger bag. I often pay for coat/bag check, too. I don't know WHERE all the stuff creeps in, but I'm really prone to the bag-lady look if I'm not vigilant at conferences.

Although a lot of attendees at the conferences I go to tend to wear full-field gear attire, including expensive outdoor brands and zip-off pants...like they are about to go stride up the mountain. May I could get my own alpinist backpack and embrace the look. 

You haven't taken trig and you want to get an MS in statistics?
 
What makes you think you can even handle a MS in stats let alone do one during a PhD ? 
 
What does doing an MS get you that self learning doesn't ?
 
What you call advanced math most people take in High School (if you consider trig and calc 1 and intro statistics advanced). 
 
Wouldn't you be better spent developing and working on your dissertation? 
 
These are  some questions/comment you should be answering and thinking about

I think you will have a very hard time getting into even an unranked program, unfortunately.  Even the GPAs at mid-tier programs have above 3.0 (probably above 3.5). For example, the program where I did my masters (funded) accepted people into the program that weren't competitive enough to get funding in our program, and they have 3.8 GPAs ! While a lot of earth science programs are forgiving of GPA, your GPA is actually below the minimum for graduate school (not departmental, university wide) at most places! This means that for the department to accept you into the program, you will need someone on the admissions committee to appeal the graduate school in most places.  This is possible, but you have to give them something to really make it worth their while: your statement of research (or purpose) must be immaculate.
 
I say this as someone who has a low undergraduate GPA (3.05) (I was also a physics major) but had a great deal more research experience than you at the time of applying.
 
Think about what you can leverage: do you have strong skills in your desired field? What about professors, who are writing your letters, do they know anyone who might be interested in speaking with you? I think the key is getting the people you want to work with to want you as a graduate student so they can vouch for you on the admissions committee and then appeal to the graduate school. Of course graduate schools have their own process, but this seems like a common path. 
 
Your GRE should be as high as possible yes, but it won't make up for the fact that you have a below than required GPA.  It seems silly, but even the .23 increase in GPA would have made getting your app into a MS program a lot easier. 
 
You might get lucky and find funding, but I'd expect to pay for a MS program, even at an unranked school. 
 
Goodluck.
 
Edit: http://academia.stackexchange.com/questions/324/how-do-you-get-a-bad-transcript-past-ph-d-admissions
 
has good advice

If you contribute money to a school, and then your kid is rejected, are you more or less likely to keep contributing to that school?
 
Also:
 
http://www.forbes.com/sites/joshfreedman/2013/11/14/the-farce-of-meritocracy-in-elite-higher-education-why-legacy-admissions-might-be-a-good-thing/
 
vhttp://www.businessinsider.com.au/legacy-kids-have-an-admissions-advantage-2013-6
 
This isn't empirical proof, but the logic is sound. I'm not sure that universities would want to release this information. 
 
I think the proper solution is to make sure that there are elite public schools that can help upward mobility. The problem is these public schools are now becoming just as expensive as the elite private schools, but that's for another thread. 

This is good advice.
 
Can you do this while being ABD?
 
Not to come of like a hardass, but again the math you have taken is nothing like linear alegebra with math majors. Plenty of people get As in math in HS. I think its a bit premature to be considering a graduate degree in math when someone hasn't taken any college math to begin with. 

These things are not mutually exclusive. Considering legacy status does have the effect of being racist and classist at elite schools, since non-white students weren't admitted to most of the ones that care about this until the 1960s at the earliest, and even now non-white students represent a minority of students on campus. It's classist because elite universities that care about this are typically very expensive and the ones who tend to have legacy also come from wealthy families.   However, I'm pretty sure it's true that legacies do give more. I don't have proof for that, nor do I want to find it, but the reason I'm pretty sure it's true is that universities wouldn't offer legacy preference in admissions if it didn't benefit them in some way. Some schools are open about this; Stanford, for example, checks to see if the parents of legacy candidates have "maintained their connection to the school," i.e., given money. Aaaand that in turn engenders more money. If your son or daughter attends your university and is reliving all the same traditions that you lived XX years ago, then you relive them too, and maybe your nostalgia motivates you to donate.   Does that trump the disadvantage that legacy preference puts non-white students and poor students at? No. Am I saying this to defend the practice of legacy admissions? No. Of course university admissions are unfair; they would be even without legacy admissions. That doesn't mean it doesn't have some advantage for the student body lucky enough to be there, legacy or no.   Anyway, the answer to the original question depends entirely on the university. At most universities, I'm guessing the answer is no, postdocs don't count. The reason is embedded in the above - legacy admissions exists primarily to drum up more monetary support and preserve traditions (which may also drum up that $$$). Undergrads obviously are the focus of that experience, so undergrad legacies are important to many elite schools. Graduate students at some elite universities may also feel strong ties because their experience, in some ways, mirrors that of the undergrads. For example, elite law and business school grads often form tight-knit networks and have traditions of their own that may engender giving, so universities may see an interest in extending a slight bump in admissions to the kids of grad student alumni, although it's probably not as big as if you were an undergrad. (This is exactly what Columbia, my graduate university, does - small bump for kids of grad alumni; bigger bump for kids of undergrad alumni. And honestly, I have to say that I do feel a certain kind of connection to Columbia, even as a grad alumna.)   But postdocs are far more like employees than students. I'm a postdoc at Penn State and I don't know much of anything about their traditions and experiences, nor do I really care that much. I am not inclined to donate money to Penn State, and I don't feel warm fuzzy feelings towards PSU as a university. It's a great place to work! But I don't have nostalgia about it. And they probably know that, so why extend legacy preference to my kids when they're not going to get anything out of it?

No one will ever like you with that attitude, no matter how prestigious of a school you go to (and UCSD is very prestigious) you cannot succeed acting like that. Perhaps academia is not for you.

I'm sorry you feel that wasn't advice. There are other options besides going to graduate school and paying. Going into a program where you must research and take out loans is a type of stress you should not consider. You are destined to fail. Some people come through ok, but many don't. Research is a fickle thing, sometimes it works out, sometimes it doesn't. Do you really want to wrack up debt on something that variable?
 
I'll let you know that I also switched fields, got into a single funded masters program and used that to leverage myself into the PhD program of my choosing. you can do this too, I had terrible grades in undergrad. Luck plays a role, figure out a way to get lucky.

I think the general advice is sound, but there is a lot of conflating it, lets break it down. 
 
In the workplace, the boss determines how work should be done. You were paid for hours you did not complete. Therefore, if you cannot do the work that the boss wants, in the way the boss wants it, you should give back the money.
 
This is not complicated.

I'm sorry you feel that wasn't advice. There are other options besides going to graduate school and paying. Going into a program where you must research and take out loans is a type of stress you should not consider. You are destined to fail. Some people come through ok, but many don't. Research is a fickle thing, sometimes it works out, sometimes it doesn't. Do you really want to wrack up debt on something that variable?
 
I'll let you know that I also switched fields, got into a single funded masters program and used that to leverage myself into the PhD program of my choosing. you can do this too, I had terrible grades in undergrad. Luck plays a role, figure out a way to get lucky.

I would not pay for a graduate degree, especially one that involves a thesis. 

I don't think its good to think that just because one situation is shitty another place should also be shitty. That is essentially your argument, in case you want to revise.