Do the timing marks coincide as shown in the small diagram?
What do the spark plugs look like? Are they secure (not unthreaded loose - do NOT overtighten them)
Since you are in there anyway ... are all of the valve clearances within specifications?
Is the exhaust header properly secured to the cylinder head? Leaks at this location can wreak all sorts of havoc.
How's the air filter?
Does the engine have good compression? If you don't have a compression gauge, you can feel it when rotating the crankshaft with a socket. It should go between tough and easy twice per revolution and each tough bit should feel about the same. This isn't a substitute for a proper compression measurement but if something is grossly out of whack, you'll feel it.
Drain the engine oil and look for evidence of metal particles in it. Take the oil filter out and cut it open, looking for the same. If you've spun a bottom end bearing, the oil will look like copper metallic paint ...
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