Good idea with the charger; I only have a trickle charger, but could maybe borrow one. That said, I finally got around to checking some readings. Stator output was fine. R/R diode check indicated failure. It does not appear that my failed R/R is affecting the charging system by either overcharging or under (not) charging the battery. I guess it's possible that it is simply not putting out enough voltage at low RPM. My battery also indicated a voltage drop on a bench load test, so first I will replace the R/R, then if not 100% corrected, will replace the battery. It is aging and was discharged several times during diagnosis, so would not hurt to replace it anyway.
Jetting - The dealership thought they had found the problem when they replaced the CDI, but when they found that it still idled rough, they figured mixture issue, so pulled carbs, cleaned some carbon on one side (from misfires?) and upped jets from 120 to 122.5 (or possibly 125, I can't remember right now) and 40 to 42. My bike is stock except for I removed the AI. When I told them that, they said I should have upjetted, which is one reason why they did it. I didn't think that was necessary, but I do believe my bike was lean before. With ignition issues getting in the way, I don't know if she's rich now or not. Plugs have looked ok, but I haven't done a lot of riding because I don't want to run her till I know things are as they should be. Before all this happened, this was supposed to be the season I was going to try removing 1 baffle, going with a K&N and jetting accordingly. With any luck I can move on to that after replacing the R/R.
Thanks for all help! Mike
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Mike, to maintain continuity try and stick to one post. It helps with the bigger picture.
In the first link above you stated that the dealership upjetted your bike? Why? If it ran good before, upjetting to address a symptom could cause future problems. You stated that the bike started fine with the choke on originally but you always needed the choke even after a short stop. I agree it sounds like your bike was lean but it wasn't a problem for you. Having said that, when properly jetted, these bikes only need the choke for the initial start (depending on temp).
For me (after the initial start/choke sequence) any start, even a couple of hours after the original, wouldn't need it. Also, you should have good drive ability with the choke on, other than a slightly higher idle. How big did they go with the jets? What is the config of your bike (exhaust, intake)? Your bike may be so rich now, that you don't need the enrichener any more and you also have the Procom variable?
