most electric problems are because of a mechanical failure. Have you checked all the plugs/connections are clean? Not just the generator and reg/rec ones, also the handlebar switches etc.
I have a powerscreen engine with standard 4-2 exhaust from an 1100L, carbs and airbox from a 750L. K&N filter in the airbox, 142,5 main jets in the otherwise stock carbs. 3 degrees ignition advance.
Runs quite well, pulls all along the rev range.