1. The carb's pretty much line up with the cylinder they go to. The left carb goes to the left/upper cylinder and the right carb goes to the right/lower cylinder.

2. The heads should be cleaned up when doing a top end. They dont' really build up carbon like your power valves or exhaust will. I generally use a contact cleaner and a fine 00 scotch brite pad with almost no elbow grease the head is shiny as new. Now the flap valves and exhaust take a little more attention.

3. Silicon should not be used to replace the head gasket, or base gasket. Stick with the paper gasket for the base gasket and the metal gasket for the head gasket.
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Charles Gallant