Motorcycle Repair: hesitates and misfires, intermediate jet, stock carb

Question
Upgrades including S&S E with intake, HC pistons, heads have been worked, cam replaced, Rivera Pro clutch,  Accel plug wires.  
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-----Question-----
I just got an 89 FLHT with 28K miles.  When I am riding and I come to a stop for any reason, the bike hesitate and pops when I start going.  It will do this for a short while and work itself out.  Does this all the time.
-----Answer-----
Stock carb and stock ignition?
Mike

Answer
I would start by checking the intermediate jet in the carb. First, turn off the pumper on the carb. Go for a ride. Keep the RPMs under 3000. This will run the bike on the intermediate jet. Ride for about 5 miles. If you get poping out the carb or it bogs then you are running to rich and need to go smaller ont he jet. Spitting out the exhaust and you are to lean. Also, you can try retarding your ignition slightly.
Good luck and happy riding
Mike