She was lethargic, spent nearly the entirety of it battling nausea. She cried often and several times wailed that she felt trapped. She didn't instigate fights, but I still felt like she hated me. She closed herself off to me, she stopped making jokes or laughing at them. We used to talk for hours everyday but during this she didn't seem to want to talk at all.

There is something called perinatal depression which is includes postpartum depression, and it refers to depression both during and after pregnancy. It's very possible that due to all of the health issues she experienced, she had depression during her pregnancy.

I don't want to suggest that you dismissed her feelings, but were you as supportive as you possibly could be? Maybe she felt resentful that she was the one who had to deal with all of these physical ailments, and you got to still be you. She likely did not want to tell you how she felt because of all the hormone changes and her own internal struggles.

She barely makes eye contact with me. If I enter a room with her alone she'll find a reason to tend to the baby, even if he's sleeping. She used to be very physically affectionate towards me, but no longer.

This again sounds like she is harboring some major resentment. Talk to her and find out what is wrong, what is bothering her, and don't make it about you and how you feel (even though I know you must feel really terrible due to her reaction to you). Try to focus on her, tell her that you love her and love your son, tell that she is a great mother, but it seems like she does not seem to want to be affectionate toward you. Ask her why, and ask her how you can help her.

Having a new baby is a huge change, physically, emotionally, psychologically, hormonally. I remember going insane when I had to tend to the baby and hearing my husband play video games downstairs, even though it was completely normal and something that had not bothered me previously. It is perhaps irrational, but new mothers need a ton of support, and if you have not been there for her as much as she perceives you could have, it might have led to her shutting off from you.