Let's see if I can remember everything I want to say:
1) definitely have her checked medically. Crystals are something that usually require a special diet FOREVER in order for them to not return. Has she been on prescription food?
2) get a product that is an enzyme cleaner specially for cat urine. Soak, and I mean SOAK the pee spot and allow it to dry. If you can borrow a machine that extracts water (like a bissell little green clean machine, or full sized carpet cleaner with upholstry attachments) use it on the spot after the enzyme cleaner has has a time to work.
3) The rubber bed sheets to cover the furniture is EXACTLY what my vet suggested to me in case of further accidents (as you know I am combatting a bit of a peeing problem myself).
4) if it is not medical (but I'll bet you it is) you may have to do like I am doing and confine her to a small room for about 2 weeks to retrain her about the box.
5) when you brought Lilly in, did you add another litter box? And even if you now have 2, you may need 3. (I have read many time to have 1 MORE litter box than you have cat)
6) and most important, GOOD LUCK !