Good input guys, thanks.
Got her all back together and rode to work yesterday. Man, what a difference! I think that broken thrust washer was really putting some sand in the vaseline. The bike had a pretty unpleasant band of vibes at 60-65. Luckily it was smooth at my normal 80mph cruising speed. Now it's smooth everywhere! The mirrors are crystal clear at all speeds and really no vibes at all in the bars. I think I have a good one.
I replaced the o-rings on the throttle body air bypass screws and put the screws back where they were. I wish I'd checked the balance before I took the bike apart, just to see if it made much difference. They needed very little adjustment to be in sync.
I had new tires mounted while I waited and ogled new bikes at A&S (actually, I'm always more excited to see what's in the used section!). Stared at an R1100S for a little while. I bet it's fun, but I like my K. Tires are Michelin Pilot Activ in the OEM sizes, it's hard to compare them to the old, cracked Dunlops they replaced...1000% better, of course.
Rebuilt forks, slick clutch, way nicer gearchange thanks to those clean splines...she feels like new again. I swear I can't feel a single bump through the forks, it's amazing what an oil change can do. Can't wait to see if I picked up any MPG benefit with the cleaned injectors.
Before the tear-down, the handlebar was really mushy in its mounts. I took things apart and compared them to the fiche, and found that there was supposed to be a washer on top of the upper rubber mount (under the handlebar clamp), mine were missing. Maybe someone took them out to try to tame some vibes, maybe the factory forgot. I bought new ones and the bars are so much more solid, no flex, much nicer steering response and the vibration is less than before, if anything.
I flushed the brake fluid but could not get more than a few drops out of the rear caliper. I played around with it for a while only to discover that the dealer-installed reservoir update (mounted behind the side cover) was done wrong. The reservoir has two outlets, one is blocked, the other isn't. The feed hose to the master cylinder was connected to the blocked outlet! Whoops. Fixed that and had the brake bled in two minutes. If you want it done right...