Thank you to everyone for the advice!! I've been rolling this problem around in my head a lot, and I think that for the time being the plan will be this:

First, to get her a really tall cat tree with a hidey-hole at the top so that she has a refuge from Sherpa.

Second, once this foster dog leaves (her permanent home is picking her up at the end of the month), I'm not taking on any more fosters. It's too hectic for me and Charlie both. I love this foster puppy, but I'm sick of her too.

Third, I'll keep making sure she can get away from Kyubey by blocking off the upstairs for the time being. We'll keep using the feliway also.

There's no way to shut the kitties in separate rooms unfortunately, because we're in a loft. Sherpa can easily jump the cardboard barrier that keeps Kyubey downstairs.

I've tried a "calming collar" on Charlie before, and didn't notice anything except that she found the collar uncomfortable for the entire month. Has anyone tried tryptophan based calming treats? We sell these at my work, but I haven't had any feedback from customers so I just don't know how well they work.

If I don't see a noticeable difference in her in a few months' time, I have a few ideas of where to start putting out feelers for an only-pet home. My grandparents life in a senior mobile home park and may have friends there who would love a cat. I have a lot of customers who do rescue and may have contacts to help me.

I don't actually think the cystitis would be a huge stumbling block. It's VERY easy to tell when she's flaring up (she starts to pee in the sink) and VERY easy to treat. Actually, since I switched her to a fish-based kibble in the morning and wet food in the evening, she's only had one flare up in a year's time!

I really don't want to see her leave here. She's my bunny-soft, squeaky little lovebug. I just don't want her to be unhappy because I want her around.