Motorcycle Repair: Carb jetting, air fuel ratio, stock pipes

Question
96 fatboy, stock motor, @ 60,000 miles, kuryakin hyper charger, stock pipes with one baffle removed from each pipe. Indy rejetted at the time baffle was removed, unsure of jets.  Runs Ok, little flat in the mid-range, carb farts at times, little puffs of black smoke if you rap the throttle a couple of times.  Pulled plugs and they are a dry sooty black.  Question: Are there things I could do to try and correct these problems or would it be best to have it dyno tuned?  It not a real bad problem but I would like to fine tune the carb to get it as close to perfect as possible.  Have been told it's better to be a little rich rather than lean.  I just like having things as close to perfect as possible.
Thanks

Answer
your bike is to rich on the main jet and too lean on the idle jet, spit back throught the carb is a lean condition, black smoke out of exhaust is a rich condition, install a good set of exhaust. like a white brothers e-series 2 into 1 exhaust system and gain 10 to 12 horse power and torque across the entire power band, and have it dyno tunes on a load controller dyno with air/fuel ratio montor, get rid of the hyper charger air cleaner it is good at killing horse power and torque.  JOHNNY