Here's my thread on the rebuild of the bottom end:
http://www.pilotodyssey.com/PO/viewtopic.php?f=26&t=13605You'll need a couple special tools (bearing push/pull press, bearing remover, flywheel tool), but its nothing out-of-this-world. Bearings are easy, but one of the most vital things in the 2-stroke Engine. Nice thing about the FL350R
Engine is that [1] the center cases use an actual gasket -- not just the basic Honda-bond sealant, and [2] the guts are about as basic as it gets with no transmission, shift forks, ball detents and such to worry about.
You can get a good look at the crank bearings once you get the oil seals off. Look for pitting, corrosion, missing pieces, etc. Sometimes you can even hear grime and grumbling made by worn-out bearings.
Check the crank for run-out (aka: "crank wobble"). If the prev owner thrashed a crank bearing and/or had a run-away death-rpm and/or some nasty detonation, they may have induced some run-out. You generally check it with a dial indicator and set of v-blocks (or good lathe chuck), but you can also see "bad" run-out with your naked eye. You can even just tape an unwound paper-clip firmly and rotate the crank to check if the gap between end of wire and the shaft changes. Also look for signs of past "events" such as scrapes, scratches and sometimes even prev builder's initials.
Check the top-end job including the lube holes, exhaust bridge relief, and measure the wall clearance (gap between piston OD and bore ID) to make sure its not out of spec. Check ring gap to spec.
Get an all-around look at the crank pin needle bearing. Look for pitting , corrosion, missing needles, etc.
Get a good look at the rod's wrist pin loop with the wrist-pin out & piston removed. Look for hairline cracks, shaved material, surface imperfections, etc.
Get a good look at case damage, cracks, repair-jobs, etc. Assembled the empty cases together, light the inside with a flashlight, and look for dings/waves on the center sealing surfaces.
Get a good look for any signs of water-intrusion. Look for one half of the crank lobes to be corroded. And when you pop the recoil cover off, that stator and flywheel should look CLEAN.
The best thing you'll get out of a total rebuild is piece of mind. Once you know everything is good inside all you need to do is ensure its sealed up (no air leaks), setup the carb right, break it all in properly, use good fuel & oil, and have fun.
Once you get the Engine running great, the next you'll want to look at is BRAKES. Going fast is fun...until you need to stop, lol.