Like a chef, we're only as good as the ingredients are. Seems like you're on the right course though. I doubt the new stator will be a problem, should have nice shiny copper windings of the proper diameter and length... I should know better, but I don't have any newer toys :| My cousin's got a huge ass quad thing in the garden shed, but that's his to break and fix.
Could always be worse, how'd you like to put a 100 lb starter in this thing? http://www.newgrounds.com/dump/item/5c5351a3e8c6e9ede29addf5b420c69d eh, only the flywheel's showing on this one... the cover got blown off ours a while back, badly dented by the brush-hog.
VicariousE
Erm... kinda skimmed this, but you've got problems with a (de)magnetized flywheel? I thought most bikes took points to power things.. ah well, I've only worked on old crap, magnetos, carburetors and such.
Hope the new voltage regulator works okay, I've had problems with them in the past, engine doesn't run as smoothly :| If you've got an imported bike, should be no problems though... it's the American metal that requires domestic replacement parts... the knocked off aftermarket stuff from overseas, is usually repurposed crap :\
Galneda
Not sure about a flywheel, but its a Stator. It uses the kinetic energy of the moving parts of the engine using magnetism to generate power...like an alternator, but stationary (hence its name).
I'm kinda concerned, though, of the origins of this new stator I've put in...no telling if it'll be a troublesome aftermarket part...but, theres no doubt in my mind that the one I pulled OUT of the bike has been there since 2002, so its possible I may have prevented a headache from happening in the future...just in case though, I'm keeping the original stator in a box, safe and clean.