She slept in the bed again last night, but announced it was only because she was "afraid she might die from the paint fumes" in hers (I think they are doing work next door).

tell her enough with the comments... you're not ready to be with her anyway... she can always sleep on the couch if she is so unsure of you...

She talks about wanting to feel like she can breathe and be apart, but how it can't happen when we live together because both our feelings get hurt. If I do things on my own, she feels abandoned. If she does her own things, she feels guilty. I feel like she has so many "wrong" ideas...and then I remember how she always felt I think she's wrong.

so what... if she is wrong, she is wrong... tell her there is no reason for either of you to feel guilty whenever you do separate activities... you're cool with it... and she should be cool with your doing your own stuff too...