Here is where I'm at now:
I replaced the ignition module($255 OEM) a few days ago and got the timing squared away on this yesterday. I replaced the ignition coil($33 OEM) and spark plugs($7 Advanced Auto Parts) yesterday and adjusted the Carburetor to 2.5 turns out. As of right now the bike is running without stalling or spitting black smoke. However, in low RPMs it is still sputtering a little bit. I have to rev it up at a stop and slow down to keep it from sputtering too much. I spent hours last night adjusting the carburetor from 1.5 - 3.5turns and I can't find the sweet spot. My carb is jetted with #45 & #175 jets.


SIDE NOTES: the timing cap is riveted on I assume to keep people out. You're going to have to drill these out and replace them with self tapping screws.. unless you own a rivet gun. To replace the ignition coil you need to unbolt the gas tank/speedo and lift the gas tank up a couple inches. This allows you to remove the bracket for the coil and ignition. Unscrew the ignition (because it blocks one of the bolts for the coil) and then unbolt the coil. Reassembly is pretty easy.

 

I have had similar problems recently except mine will backfire and shut down as well. Did you figure out what your prob was?