I learned that the standard idle mixture screw setting on this bike is 3 turns out. Currently, they are set at 3 1/2 turns, and the bike runs great! Perhaps that extra 1/2 turn compensates for the aftermarket slip-on muffler. Those tend to lean out the mixture condition, from what I understand.
I did order a vacuum gauge kit so that I can sync up the throttle valves, and also make sure there is no intake leak. Either way, I consider this project to be complete. Thank you all for your help.