Jon - have you had the airbox apart, yet? Â I was wondering if you have checked for mice nests. Â You will probably want a fresh air filter, anyway.
I use Hucky's for most maintenance items, but since he doesn't really "do" R65's, he may not have the push rod tube seals, since they are one of the parts that are unique to the short-stroke airhead engine.
For ignition wires and sparkplug caps, I go here:
http://www.mikesxs.net/products-27.html#productsUse a soldering iron and remove the soldered-on tips from your original wires (the ones that go into the coils). Â Reuse them on your new wires. Â Much more better than the crimp-on type.
Drain your transmission oil ASAP and check it's color. Â If it is milky, it has water in it. Â You will need to replace the rubber boot on the speedometer cable, as that is where water enters. Â Some put some grease inside the boot to stop water, others put a wire-tie around the top of the boot, and others use a large piece of heat shrink.
Check the magnet on the drain plug for metal bits. Small fuzz is normal. Large pieces are an alert.
Take care with that bolt that holds the ground cable to the transmission. Â You don't want to strip those (or any other) fragile aluminum threads in the case with the steel fastener. Â That bolt is also the vent for the transmission, and it should have a hole drilled through the center. Â Check it for blockage. Â This same fastener also holds the speedometer cable in place.