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Kinda flukey to have an ignition problem coincide with a top-end R&R....I'm first suspecting a grounding issue on the engine (can it produce such symptom??) and then a broken pick-up wire lead (engine R&R thing that is electric/ignition related)
For anyone looking for an answer.
I found a crack on the top of the right carb that was causing the diaphragm to not seal.
I used some JBweld to seal the crack.
Bike starts, runs and revs like new.
They must have been dropped at some point. Very odd to be sure. I'm happy I inspected them so closely or I'd still be messing with it since the bikes timing was spot on.