shit thrillseeker! I've got two pages of the EXACT SAME issue, EXACT SAME bike, on another forum (VJMOG) and still no resolution. I have replaced coils, high tension wires, spark plugs, electronic ignition (yes replaced it) and ran new fresh wires to and from the ignition/coils. New ignition switch, new battery, new regulator/rectifier, and still have a wonky spark on the R/H cylinder (weak and sickly yellow) been through my carbs at least a dozen times, and replaced the petcock as well as the fuel tank, and the fuel lines and new filters. the only difference I can find between our bike problems is that mine only happens after a good hard run down the slab. Around the neighborhood I can putter round all day long! WTF?
caveat: a have spoken with a few people that swear the keihin carbs on 360s are far too fiddly and life is easier by just replacing them. I'm still in for solving the problem...