Only firing on 3 cylinders

If 2-3 are not firing, but 1-4 are. I'd swap the coils around. Remember it is a Wasted Spark System. So if you have one bad plug or wire or cap, it can lose both on that coil.

Had similar problem a couple times. Solved one when that carb's pilot circuit was cleared of obstruction.
Recently had malfunctioning Dyna 2000 ignition module. #1 & #4 not firing. Sent to Dynatek for testing and module was replaced under warranty. Larry Nelson at Dynatek has been very helpful more than once.

Well I'm 99.9% sure it's not carbs. I had them off once and they looked fine. All new plugs and wires so.....

When you say looked fine, did you blow air and carb cleaner through the carb pilot circuit? You would still have fuel at open throttle though. So maybe it is something ignition. Motorhead suggests swapping the coils, which would isolate the problem to something in that system. That is how I isolated the recent problem I was having to the Dynatek module, because the swap made absolutely no difference. Then I called Dynatek...
That is my two cents. Happy hunting.

When I took the carbs off I only went through number 2 cause that was the only cylinder I was having issue with. Sure would be dumb luck to have pilot circuit plug up on 2 and 3 an lets say not 1 and 2. Either way I blew out number 2. Has to be ignition. I'm still in Florida so I won't find out till Wednesday.

well here I go, replaced the coil and low and behold same thing 2 and 3 were still cold! So started in the ignition cover opened up and everything was in tact. traced the 4 wires back to ohm out the pulse generators and guess what? The 4 pin connector wasn't seated and wasn't making good contact on the 2 and 3 wires. That explains why it was loosing power in the rain! Guess I have an extra coil now. So lesson learned. Go through everything before starting to buy parts!Bike fires right up and runs like a champ again. Thanks for all your help guys.

bromz wrote: The 4 pin connector wasn't seated

where is this located exactly? pictures help!