Thank you for the kind words!
You are absolutely not reading too much into it: it's intentionally incredibly dense. However, I'm a big post modernist, so whatever you want to take away from it is valid.
*spoiler warning*
The one question I will answer definitively is that the thing that comes out of the CT machine is just... also Elly. It's allegorical, but it's an allegory specifically for autoimmune illness, which is my particular flavor of chronic health problems. The exact diagnosis is never made clear (intentionally) but the doctor notes underwater point to autoimmune if you know the medical terminology.
Because something went terribly wrong, something that you *know* to be your own body is being perceived as alien and awful and needing to be destroyed. Elly isn't sick because she has something foreign inside of her, she's sick because she is unable to recognize that thing as just her. To try to destroy the other without acknowledging it as a part of yourself is tantamount to death, and the "correct" choice is to simply... coexist with it.