Ron: I haven't noticed any idle noises from my Mikuni - could you have worn slide guides?
Doug S: if it is an Andrews EV-3 you have the specs look ok for a mildly trimmed bike. IMO, if all cylinder parameters & tests, intake & ignition parts are checked out ok this is an odd problem. I don't really see how it could be a cam gear timing issue either - if so, both cyl should be equally off, plus you're saying it runs great at higher rpm's...
I assume you've checked your pushrods, although again it should then get worse at higher rpm's...
My money is on the carb, and here's a theory to chew on:
The rear cylinder cycle is 315 degrees after the front, while the front is 405 degrees after the rear. The carb therefore has more time to supply its A/F charge to the front than the rear, and if the carb is a bit worn somewhere it could show up as a disturbance at idle...