Just a hair off isn't likely to cause a huge deal, i have actually had ones that i couldn't get perfect just how the sprocket/chain/cam line up they are not 100% perfect. All you have to make sure is the ignition timing is right and that you adjust the pickup coil/aka pulse gen to line up with the advancer when its set to the F mark on the flywheel.
My guess would be running lean since your idle is also erratic. Check your intake for cracking, did you replace the o-rings on the carb to intake and the intake to the head? They are generally flat and hardened and need replacement. Pull the plug and read it, see what you got for color.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....