Kevin,
We all suffer from not having the best mechanic at hand. Last year 5 of us took our FJRs to Powers Yamaha in Salem/Sublimity to get valve jobs. They gave us a nice deal. I would take it back there now as my original service center closed (Action in Vancouver, then Action in Gresham). Other then those guys, I haven't tried any others. I do most all the work myself except the valve adjustments, but when I do the valves, I usually add other things to the work list, like brake lines, coolant, etc.
Come to Busters today at 4-5pm for BBQ and meet others that maybe able to give you more guidance.