1999 Yamaha V Star 1100 Custom "motorcycle hesitates upon acceleration" Questions

What causes a hesitation upon accelerating on my yamaha vstar 1100 custom. I changed the plugs, changed the oil. The only thing I didn't do is change the gas that is currently in the tank. The bike ...

...hesitates when not accelerating, and backfires upon decleration.I have changed the plugs , fuel filter, had a mechanic cleaned and rejet carbs. The bike came with cobra pipes, no baffles, i bought ...

...upon acceleration and deceleration I can hear and feel it hesitate and pop. I know I have to change the main jets on the carbs but was wondering how much bigger should I go? I have read that the ...