I'd just start with the exhaust side. Wait until yo see what's going on before you start looking for sources, a chewed up shim can be had from a Yamaha dealer for just a couple bucks, but the cam shaft that it murdered would be cheapest to source used and then have polished if needed.
When you reinstall the valve covers do NOT over torque them! The spec is for 22 INCH lbs... not 22 ft. lbs. Too much and you can warp them and then they never seal right.
No need to drain the oil when pulling the valve covers. Just clean the engine around them so you're not knocking 20 years worth of grit into the engine.
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