Ive done this job many times...... Here are a few things to consider
plugs
check coils for rust / damage
check steering bearings and races
cush bumpers in the rear drive / rubber
wheel bearings if this has not been done
remove swing arm and lube the splines and all bearings
fork maintenance if this has not been kept up
clean and lube throttle tube
check the bolt that holds the bracket - that holds the whole front end on. It sits just under the ignition. Check this part for any cracks
check spokes
check rims for cracks (near the spoke head)
replace the clutch #24-25-26 on the schematics, if that's not been kept up
I would also suggest the push rod from the slave cylinder over to the clutch (ball)
clutch reservoir rebuild kit
look at and inspect the piston in the clutch slave cylinder, make sure its still smooth (straight) in the bore. They will start to get sideways at 100K +
all brake and clutch fluid
make sure all the rocks and leaves are out of the ABS box so it will drain
check the front seal / rust on the front of the diff after the diff has been removed from the swing arm.
check / double check the TB sync (back out 3/4, Etc)
check rotor thickness and pads, etc. front disc should be good, you might need another rear
check and clean the ABS rings on both wheels
check and lube all the lower suspension when re installing the swing arm
radiator flush
eye-ball the clutch pressure plate along with the first 4-5-6-7 clutch plates
while checking the air filter, pop out the two bottom plastic pens on the dirty side, so water can drain, one on the L & R
If you have aftermarket exhaust, pull the headers and re seal between the head and exhaust tubes
if you have aftermarket muffler, re pack muffler
BTW- I recently performed a valve check @ 125K and adjusted 7/8 valves. While I was in there the guy bought a new timing chain and wanted it installed. I replaced the chain and noticed the cam gears to look virtually new with close inspection. Extremely low 'wear', so little I don't even want to call it wear. It was actually just a very slight polish only where the chain actually touched the gear. At this rate it would probably go 500K+ miles.
Anyhow - I checked the new chain against the old chain and there was a pretty major difference in length. Admittedly, I did not Mic. the difference in length, but it was probably 5-7mm difference in length. I also made note that before the disassembly the Graves MCCT only had 1/2 - 1 thread left remaining. After the new chain it had about 10-12 threads on the MCCT. I also checked the wear pads that ride the chain and there were no excess wear and looked totally normal. So no unnecessary strain on the chain prior to the change.
Is the new chain required? Probably not. But I will say that after the chain and work, the motor was more snappy. Of course this is my perspective after working a million of these. The chain is not expensive and for folks with 100K+ miles might want to "consider" the new chain with your next valve check. BTW- for the DIY guys, you dont need the special yamaha tool to torque the lower gear back onto the crank shaft, you only need a small bar of copper or aluminum.
Just another thought for the high mile guys running a stock CCT. I noticed the 'used - throw' on the Graves MCCT when this chain had been stretching. For folks using the stock CCT with a high mile engine (stretched chain), could the stock CCT run out of "throw" (pressure) on the chain? I wonder if a high mile engine had a stretched chain and a stock CCT it could eventually loosen the chain (lack of CCT pressure) and then possibly cause excessive engine noise or even cam skip ?
If I ever get to 100K I will toss one on just to keep the mechanical precision the best it can be. (Ive also stated a thousand times, dont be a follower and read garbage on the internet, check your valves. And if they get adjusted request the 'before and after' clearance numbers before you get the work done. Get them checked "don't be that guy".. I can tell some stories for sure)