Geo,
As others said above, check the mechanicals; pivot bearings, wheel bearings, bent rims, rear lug bolts, then the shocks, fork tube oil (for lube only), steering head bearings, handlebars, etc. Most of these can be checked by you by wiggling wheels and things. Make sure you don't have a dragging caliper, too.
Also, check the tire pressures as suggested above. I run 36 and 42 cold, but installed a TPMS earlier this year and am amazed at how much the pressure fluctuates - as much as 5 psi - as the tires heat up and the day warms up, so you don't need to be extra precise 'cause it won't be that pressure for long.
Tires DO make a HUGE difference. Saying "Michelin" is like saying your car is a Ford. The Michelin PR4's are the gold standard for me. Working on my third set on the R11S. So what flavor Michelin do you have??
The R11S normally has superb handling. It never ceases to amaze me. It handles MUCH better than I can drive. I have found that if I only hold the throttle with a finger and thumb and keep my left hand on my calf behind my knee, the bike will corner MUCH better and lean much farther than I will. The LESS input I give it, the better it handles. You can easily steer with the throttle, too. Change lines multiple times in any turn at ANY speed with nary a hint of protest or loss of confidence. Sometimes I'll wiggle it in a fast sweeper and it's just like doing a wiggle on a straight interstate. It just says, "so what".
Yeah, the shaft takes a little getting used to, as well as the engine torque while stopped, and the no-dive front brakes, but not a big deal.
I also found that having the engine running really well helps the handling when I installed an AF-Xied by NightRider. It lets you adjust the A/F ratio to the normal level, not what the EPA dictates. It lets the engine run like it's supposed to. Roll-on power is MUCH better, cold-natured stalling and starting is g-o-n-e gone. Balancing the TB's and injectors helps, too.
Please, let us know what you find.
Lowndes
'99 R1100S
Wilburs
AF-Xied
EV14 injectors
SJ air filter
BP Induct