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Jimmy's diagram should prove to be very valuable in seraching for this problem. I agree that this particular problem does not *sound* like a carb problem, from all that you have described. This sounds very much electrical. I would check closely all of your connectors, ground terminations, and wiring harness. If you can not find anything obvious, start jumping out switches, as you have already started. I would go as far as jumping out the kill switch on the handle bar switch pod. You should also check any fuse blocks for good contacts. Clean any surfaces with Scotch Brite and maybe apply a little dielectric grease. After that you can either start cutting open suspect portions of the harness, such as around the steering head, or start replacing components. One thing I always keep in mind is to start with the lowest cost items first, spark plugs, caps, fuses, fuel filters, stuff like that. Before I got into any big dollar components, I would pull the carbs again and make extra sure that things were spotless.
The absolute worst thing it could be is the igniter/ECU (big $$).
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