Just bought a 97 1100RT The most annoying thing I have found so far is you cant warm the bike up on the side stand. Is there a modification to bypass the stand switch so this can be done . I use the side stand more than centre.
As the owner of an R1100RT i can tell you two things...
1. Never warm your bike up on the stand center or side. You start the bike and ride off, this is stated in the owners manual. Oilheads don't like having little to no air flow over them. Letting an RT idle to warm up can cause the tupperware to melt or catch fire... Google it.
2. The side stand is poorly designed at best ( lots of tip overs ) always use the center stand. You can by pass the side stand switch so the runs with it down.
Other then that, keep the throttle bodys synced and the valves adjusted. Then enjoy riding !