Rusty, the tool is necessary. I got it from University for $30. The tool depresses the valve bucket. This gives you clearance to remove the shim.
I have some notes at home I can email you.
I ensure each intake clearance is the same and do the same for the exhaust valves. I shoot for .004 inch intake clearance and .011 inches for exhaust.
Make sure you have a good pick tool to remove the shims and also an automotive pickup magnet to make it easy to remove the shims.
You'll need a 32 mm socket to turn the crank from the left side. Just remove the two allen screws holding the inner crankcase cover on.
Drain coolant and remove radiator mounts and let it hand forward. Also remove both top heat shields and loosen the vboost cable going into the servo motor. There's one screw holding that on. Remove both side plastic heat shields and remove coolant manifold mounts. Remove both hoses going into the engine and pull manifold forward and out of the way.
Remove spark plugs and use a screwdriver to ensure piston is at TDC. I don't bother with the markings on the flywheel because mine weren't there.
When removing valve covers evenly loosen the top bolts. Inspect the rubber washers for wear and replace if starting to crack or get hard. (Huh-huh). Easier to replace now before they start leaking.
Stick rag down cam chain tunnel to avoid dropping anything down in there.
I recommend drawing diagram of valves on a piece of papers. For each valve 'X' put clearance, current shim, and desired shim. This will make it easier to swap shims between valves and exchanging shims at the Yamaha shop.
Make sure you measure the thickness of each shim with a digital caliper. Sometimes the thickness labeled on the shim is incorrect.
When reinstalling the shims make sure the marking is facing down in the bucket. Otherwise the cam lobe will wear it off.
I have a couple of emails at home saved off that will help you determine exact shim needed.
