Welcome to the site!
On the tranny - "If it ain't broke, don't fix it". Drain the oil, check it for any sort of particles. The Pilot tranny has proven to be very reliable. If you have an 89, then it has issues with getting it into gear (reverse or forward) - it was an issue that Honda addressed in 90. No biggie.
About the only thing that seems to go wrong with the tranny is the slipper clutch - and that's usually only when you've added quite a bit of HP. You can check the slipper by looking at the color of the clutch. It should be a nice, shiny aluminum color. If it's slipping, it'll develop heat and they start changing to a bluish/brown. If it's slipping, then worry about it and change out all the plates (four, as I recall) and the springs.. If not, leave it alone.
Stock drive clutch? Time for a new one more than likely. Get a Power-Bloc from ATV Racing.
I don't follow about the stop rings comment in the rear a-arms... What part(s) are you refering to? Where are these rings and what do they do?
Good luck on finding a straight roll bar - they pretty much don't exist. Pony up the money and get one of the chromoly units from ATVR. I wasn't ever able to tweak mine and I tried farily often.... :shock:
Once again, welcome to the site.