I was happy to hear that Luna is pooping normaly. If it is inflamation that is causing the problem, I know that there are anti-inflammatory pills that you can give her.

Sorry to hear that she went on the floor again, and at this point it may be a behavior thing rather then being related to her medical stuff. Maybe she just needs to readjust to using the litter box and it may get better with time. I wish I had some other suggestions but I don't. Also, 3 boxes for 2 cats is plenty.

Well, continued prayers for Luna and I really hope that you have found the answer.