Save yourself alot of trouble, I went through all the diagnostics and found one answer. http://www.baronscustom.com/catalog/display/254/index.html
This makes your bike run like a champ, note you will hear the carbs; that detracts from some of your nice pipe sound. but the but the bike runs great. you can get just the jetting and needle kit if you want for about half the price, but I figure if I am going to do all the work why not get the most bang. Baron's guys are cool because the shop started around Royal stars and they know the bikes really good. They have also convinced me to order their Star Bar. They say the bike handles a lot better. They also have a dicount this weekend of 15%.
MY bike runs very good and all the problems you mentioned have gone away.
Mandride