Motorcycle Performance problems. 95 heritage softail w/ hypercharger. Sputtering at high end of second gear?

While accelarating through the gears I have been getting some sputtering at the top end of second gear and third gear. This usually will go away after the bike is really warmed up. What are some possible causes of this? I recently replaced the plugs and it still happens. I have a kurykayn hyper charger and a carburated engine. Python III pipes. Any help is appreciated.