Responded to your post in Newbie Introductions before seeing this.
What jets are you running? You're saying it idles fine, and runs fine at high rpms (5500 + up) but will not run smooth in between?
Seems likely still a carb problem. I'd make sure the rubber diaphragms in each carb are opening evenly at those engine speeds. (A tiny hole or tear in one could be the problem)
Carb needle positions meters fuel at those speeds. Perhaps ones loose?
I'll let someone else answer the electrical questions here....