Motorcycle Repair: Twin Cam popping/stalling, mixture problem, vance and hines

Question
I have a 2000 Fatboy with ~16k miles on it. It has the stage one kit and Vance and Hines Shortshots. Occasionally, once the bike is fully warmed up, it will pop when I will start to accelerate away from a stop and has stalled on occasion. It never happens when the bike is cold or on choke.

I have also noticed that it seems very cold natured, i.e. if I let it sit for an hour or two and do not choke it when I start it up I will get some hesitation and popping.

I am sure it is a mixture problem, but too lean or too rich?

Answer
the carb is too lean. also you willl NEVER get the bike to run right or jetted correctly with the exhaust system you haved installed. Get rid of the shortshots before you make the motor blow up. Install a set of white brothers E-Series 2 into 1 exhaust system and gain 12 horse power and 15 ft lbs of torque across the entire power band over the pipes you have that are killing all your torque and horse power.
Johnny