Ok, the pickup coil, the plate with the black box on it, should go on with the black pickup coil at the top center, just center it and loosely tighten the screws, you will have to adjust that relative to the advancer part that spins on the camshaft. Now take the plug out above the recoil and slowly turn over the motor and line up the T mark with the indicator mark, just like you did to set it to TDC to put the timing chain back on. The spark advancer should have the end with the line on, the magnet side, facing the pickup coil, the black box. Now if you look at the two of them the pickup coil and the advancer both have a center line on them, so with the motor at T (TDC) loosen the screws holding the pickup mounting plate and turn that to match the mark on the advancer then tighten it down. You shouldn't have to go very far to the left or right of center with the pickup coil, if you do then your cam isn't timed right. If the advancer is off 180 degrees then you have your cam off 180, if its only off to the left or right say 10-20 degrees you might be off a chain link or two on your cam timing. Either of those are wrong and your going to have to tear it back down and rotate the cam or jump the chain. If your cam is off 180 just remove the camshaft sprocket bolts and turn just the cam and not the sprocket or chain and then reinstall the bolts. Timing these takes a few tries to learn.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....