jumping in...when you communicate with her use the "I" word to express yourself. i feel ...etc. your efforts are great to say the least. i hope you all can make it a workable living arrangement. was she commited to this living arrangement?
are the bedrooms small? sounds like you're fix her up talented. perhaps in the future you can knock out a bedroom wall adjoining another one, put a larger closet in it. you will need to see if this is feasible with the construction of the house. thus larger bedroom, more closet space. i've done this/contractor and it really worked out well.
she does sound that she's looking for excuses re the house. are you comfortable discussing with her solutions such as the one i mentioned? ask her for a list of changes to the house that maybe you all can work on together.
you sound like a nice guy. you are not a human doormat.