I think we can all confuse the hell out of you.
Dan seems to be giving concrete advice, eliminate possibilities one at a time.
To summarize as I understand it
- bike was running fine
- after sitting with petcock off starter jambed on a restart
- rocking the bike in gear allowed the motor to turn over and then start but now doesn't fire on cylinders 1&3
- occasionally firing 1 or 3 under throttle
- can smell gas while running
- compression is verified good
- replaced timing belts and still runs the same
COILS
- one coil fires 1 & 2, one coil fires 3 & 4. Unless someone switched the plug wires from 1 & 3 to the same coil it looks like coils aren't the problem. Switch plug wires as Dan suggests and you should be able to eliminate coils as the problem.
CARBS
- If it isn't the coils is sure looks like carbs. Considering how it's running I would have guessed a stuck float, but that doesn't explain why both 1 and 3 aren't firing as both carbs starting to flood at the same time seems unlikely. Is the carb linkage working properly??? Did someone stick a potatoe in your exhaust???
Jorg