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Depends what you mean by "rebuilt" if you had the engine apart, does the gearchange switch work properly, i.e. neutral light on when in neutral and display showing N, ditto reverse. Check all those wiring connectors you had off when doing the "rebuild"
Thanks for the reply.
The motor was apart. I had an issue with aligning the n position switch at first. I fixed that and all lights and gears work. I have it running and can ride it with only the manual shift.
I am in the process of going through the connections. I have also tried to swap out the brain and that didn't change anything either.
It sounds like there is a connection issue with a couple of pins potentially in contact.
More likely a wire close to one of the plugs shorting out on the frame or another wire. When you take wiring plugs apart, you move the wires near to them and a fault that may have been there for years suddenly becomes a problem. Had a 350 last week, wouldn't spark, started checking the wires at the CDI and noticed some wires just above the CDI plug had fretted through, against a rubber breather pipe of all things, water had got in and turned two wires to verdigris.