is your automatic decompression unit functioning? does it have the right play?
sometimes the bolt slips out of the lever down under the cover in the right crankcase cover.
aligning the camshaft and the crank:
look for the marking on the sprocket on camshaft, it should align with the corresponding marking on the camshaft. the other marking aligns with the cylinder head.
same with the marking on the gear/crankshaft: there is a corresponding marking on the housing. piston should then be on upper dead point (all valves closed).
ref. also here:
http://216.37.204.3/yamaha_DB/yam_DB...1.asp?model=11
wiring diagram you can find here:
http://www.xt600.de/xt_technisches/%...plan/index.htm
regards
klaus@xt600.de