Well I bit the bullet and ordered a new motor from SBT. I've already been through the jet pump (oil change/wear ring) and electronics, so I figured I'd look on the bright side and make this a really nice ski.
All the accessory engine bits look like crap or are rusted pretty good, so I ordered a "new" (by new I mean good used condition) pto, flywheel, stator case/cover, stator, intake manifold, carb cleaning kit, and HD carbon seal kit. I'm gonna degrease the interior and replace the oil lines/filter (keeping the oil pump, I believe in Dr. Honda on this).
I'll post some pics when I've gotten it all in. Thanks for the help diagnosing all this!