It's hard to tell with just the provided information what is causing your bike to run worse. Moreover, let me know what exactly is the "running bad" symptom the bike is doing. I believe that almost all 99+ supersport exhausts will fit your bike. I bought mine from a 2003 800SS owner on this forum. Generally, you should be able to get the pipes, an open air filter and then a power commander III or some sort of tuning module to smooth everything out. The people here are very helpful, so if you just post up your concern, they'll gladly respond to you. Is this your first Ducati?
I also have a 2002 900SS but im having trouble finding post that apply to my bike. What models are enterchangable for example for exhaust and headlight parts? I purchased the bike last year and just changed the plugs last weekend but it seems to be running worse now with new plugs and i don't know where to begin looking for answers. Sorry for PM'ing you but i just saw you had the same bike and might be able to point me in the right direction. Thanks!