Did you do anything besides the Petronix ignition? Is it the original Petronix or the newer Petronix II? I did the Petronix along with their plug wire set and hot coil, and based upon a post by George B. some time back increased the gap to .032. My plugs were evenly colored light tan, which I think is nominal. How is your gas mileage? With your black smoke when you rev it, if I understand you correctly, you may have a problem in the transition to mid-range which I am sure you can correct. If you fuel mileage is good you are probably OK there in the high speed jetting. If in doubt, one of the old standby tests is to get out on the highway and run about 70 for a stretch then get off at a rest stop going into neutral and shutting down the engine ASAP; This allows you to read the plugs pretty accurately under high speed conditions. I used this test to dial in a Mukuni (non stock) on my Harley Superglide. I made an adjustment (lean metering rod on this setup) and retested. The black smoke was gone and the plugs read fine.
Whatever you do, keep in mind that this may be an iterative process which may take a little time to work out, but I'm sure it's a solvable problem. Good luck.
John H.