There are lots of over-the-counter remedies for FLUTD that might be worth trying. You could also try Cosequin, a joint supplement that also strengthens the lining of the urinary tract, but it's a supplement, so it takes a while to start working. But it also prevents arthritis.

This is a pretty good page about FLUTD. Basically, FLUTD isn't just one condition, but a catch-all name for a group of conditions that are treated differently.