indecis

I felt EXACTLY the same way after I hit send on my email accepting one of my two offers. After accepting, it took me a few weeks and a lot of conversations with friends, my masters advisor, my partner, and my therapist (and even a few posts here on GradCafe) to finally feel OK even though I knew I made the best decision rationally and emotionally.  
After struggling for weeks, here is what I figured out: I did not think I deserved it. I was accepted to my dream school, something I had been working towards for years, but for several reasons, I couldn't let myself be comfortable having it. Once I realized that, I could address the absurdity of my issue directly and now I feel confident. Based on your internal questions/doubts and your struggle with impostor syndrome (a biggie for me too), I wouldn't be surprised if you are experiencing something similar. 
But the truth is, you have value and deserve to let your light shine for the world to see. You deserve to go to your first-choice school, to work with superstar faculty, to learn and thrive in an engaging intellectual environment, and to receive compensation for your work and contributions.
When you lay out your pros and cons, program A clearly stands out from program B. Have you asked yourself the simple question of where you want to go (or don’t want to go) and observed your visceral reaction to the two programs? Your decision to choose program A might not have been as pragmatic as you believe.
Also, why do you think you are less prepared for the rigors of a competitive research program because you went to a SLAC for undergrad? I went to a SLAC. I worked for a few years and then went to a large R1 university that is top 3 in my field for my masters. I had no problems adjusting and I think the SLAC prepared me very well. In fact, I have observed (and my mentors and advisors have commented) that, in general, I tend to ask more questions, have more developed critical thinking skills, and possess a greater depth of understand about my own personal interests and goals than many of my peers. These are valuable traits and I feel I have my SLAC to thank for embracing and strengthening them in me earlier in my academic career. That is not to say that people who don't go to SLACs are not as strong in these areas, but in my first-hand experience, most undergrads at my master’s university are not getting the same attention I got from my SLAC.
I second the comment from Entangled Phantoms about finding a good therapist. It is immensely helpful and provides a level of support you’d be hard pressed to find elsewhere. I’d recommend someone who has experience working with graduate students. Cognitive behavioral therapy is very helpful in working through self-doubt and impostor syndrome issues. Your school’s health center could probably recommend someone.
So congratulations, BroHar! You made a great decision. You deserve to be at your new program and you are going to thrive.
 

At the school you are waitlist, it probably won't matter if you take extra classes at this point. If you are not accepted this year, I would recommend reading these two books:
https://www.amazon.com/Graduate-School-Winning-Strategies-Getting-ebook/dp/B005DFLJYI/ref=pd_sim_351_3?_encoding=UTF8&psc=1&refRID=P262AXW9F3X1WF2QYC5D
https://www.amazon.com/School-Dimwitted-Undergrad-Smashed-Revised-ebook/dp/B0097X0FOM/ref=sr_1_fkmr2_1?ie=UTF8&qid=1524096950&sr=8-1-fkmr2&keywords=grad+school+low+gpa
They give pretty clear strategies for getting in to grad school with low GPAs. They key is to contact potential advisors who share your research interests before applying and find a way to stand out from the crowd. Even if you have a really high GPA, if you are just sending your applications out with no contacts at a school, you are likely to get filtered out of the candidate pool pretty quickly.
I don't know what a CSD is so I can't comment on that aspect of your post...
One last note: Going to grad school because you are not sure what else you can do with your bachelor's degree is not a great reason to go to grad school. Grad school is stressful and expensive in terms of opportunity cost of staying in school versus starting a career and making real money. It also might not get you where you actually want to go in life and will not necessarily lead you to a career that is "better", more fulfilling, higher paying, etc. If you are not sure what you would do with your life if you aren't accepted to grad school this year, it might be time to take a close look at your interests and goals. Determine if you are looking to grad school as continuation of undergrad (which it is not) or if it is truly the next step towards something bigger.

At the school you are waitlist, it probably won't matter if you take extra classes at this point. If you are not accepted this year, I would recommend reading these two books:
https://www.amazon.com/Graduate-School-Winning-Strategies-Getting-ebook/dp/B005DFLJYI/ref=pd_sim_351_3?_encoding=UTF8&psc=1&refRID=P262AXW9F3X1WF2QYC5D
https://www.amazon.com/School-Dimwitted-Undergrad-Smashed-Revised-ebook/dp/B0097X0FOM/ref=sr_1_fkmr2_1?ie=UTF8&qid=1524096950&sr=8-1-fkmr2&keywords=grad+school+low+gpa
They give pretty clear strategies for getting in to grad school with low GPAs. They key is to contact potential advisors who share your research interests before applying and find a way to stand out from the crowd. Even if you have a really high GPA, if you are just sending your applications out with no contacts at a school, you are likely to get filtered out of the candidate pool pretty quickly.
I don't know what a CSD is so I can't comment on that aspect of your post...
One last note: Going to grad school because you are not sure what else you can do with your bachelor's degree is not a great reason to go to grad school. Grad school is stressful and expensive in terms of opportunity cost of staying in school versus starting a career and making real money. It also might not get you where you actually want to go in life and will not necessarily lead you to a career that is "better", more fulfilling, higher paying, etc. If you are not sure what you would do with your life if you aren't accepted to grad school this year, it might be time to take a close look at your interests and goals. Determine if you are looking to grad school as continuation of undergrad (which it is not) or if it is truly the next step towards something bigger.

For the love of God, why do people accept offers they aren't crazy about well before the deadline?
 
Boo hoo, you got an early acceptance. Stop trying to rationalize your decision by likening an early acceptance and funding offer into a stealth pressure campaign. Did want to you to accept quickly? Of course they did. Do you think they made you an early offer of admission and funding because they were ambivalent about you? They wanted you! That is OK. The school clearly told you that the deadline was April 15th. They did everything right. Nonsense rationalization is what got you in this situation to begin with. Christ!
Live with the choices you made. Don't come up with BS reasons for justifying whatever you are going to do.
As poorly as you've handled this, fuzzy is right. A PhD is a long time and you should consider what is in your long term best interest. If and when you do withdraw from the school you know informed you'd enroll at, let them know as soon as possible that you are withdrawing so that they can go down their list of applicants and get their 2nd or 3rd choice candidate. It is the least you could do even if you dread this conversation. If a phone call is too scary, at least send an e-mail. Professors are surprisingly understanding with stuff like this, especially if you are honest about your situation and timely with your response.

You're welcome! "Boo hoo" beats "cry me a river." No?