Thanks, I'll do that while I'm waiting on the crank seals, and post what I find

 

Opt, the crank seals on the clutch side seem simple, but what's the steps for the pull start side? I don't have access to a manual

 

You have to pull the recoil housing,flywheel and stator plate to get to this seal. You can "borrow" a harmonic balancer puller for the flywheel from most auto stores if you don't have one. It takes three 8mm bolts(about 3 inches long) if they're not in the puller kit.

 

Where are u supposed to mark the flywheel relation?

 

The flywheel is on a key so no problem there. If the stator plate doesn't have any alignment marks(many of the old ones didn't) scribe a mark on the plate and engine case for realignment after the seal is replaced.

 

OPt, I went to move it today to where I'm going to do the seals, and I'm hearing a knocking/rattle sound coming from what sounds like the motor. No white smoke, cranks and idles fine. Its only on part throttle or decel. What could that be? It didn't do it before the top end.

 

Also at idle the motor vibrates like crazy. Doesn't make the noise idling

Not mine, but the exact same thing mine is doing
http://m.youtube.com/#/watch?v=14HHB3qI_58

 

All the 2 strokes have a little piston "pinging" noise,BUT even with a new top end,if the bore is set up too large,the piston can rattle even louder,also the noise can be from "crunching" crank bearings. Even with new seals if the crank or lower rod bearings are worn they can make this noise, not allowing the crank shaft end to run "true and straight" which in turn can cause a wallowing of even brand new crank seals to where they can be hard to idle down correctly,still bog when on the throttle because of sucking air. What we mechanics call sounds "like marbles in a tin can". From your very first post it mentions you did a top end only. This could be the cause of the problems. That's why I would NOT do just top ends only at the shop.Plus not a bad idea to check the motor mounts to see if any have separated causing excessive vibration also.

 

Well you can't feel it, but you can see the motor shaking. It only makes the noise when it's hot. But It did kinda stumble once when i was riding at a steady speed. It makes the noise on really light throttle or decel, but only at certain rpms. Looks like i might be doing the bottom end. Funny thing is, that it didn't do it before the top end. My base gasket was kind of sketchy looking. Could that be it?

 

Leaks from anywhere can cause erratic problems,even on engines slow on coming back down to an even idle,but what you're describing is what I've found out from a lot of people when doing just top ends. What happens a lot of times is you're just putting added stress on the lower end with a new top end. Noises that weren't noticed before start to crop up. This is why I keep saying a new top end only can take out a bottom end,that is cause it to go out quicker which can do damage to a fresh new top end if the bearings separate and start spitting them out of the crank case and get to the piston area. Good $$ down the drain already spent along with having to rebuild the bottom end and sometimes having to do the top end twice! I did this twice on top ends only that came back to haunt me. After that NO guarantees unless I rebuilt the entire engine.