I just bought a 2000 Fatboy from a guy and noticed when I bought it, it had a little miss in it when you are just easing along at low rpms no matter which gear your in. If you throttle up on it, it levels out and acts right. If you run it at higher rpms, it acts right. The minute you let off the throttle and let it cost, it wants to backfire into the carb. The guy I got it from said that the pipes he put on there is what's causing it. It has short straights on it. He said the carb needs adjusting. What adjusting would it need and could I do it or would I have to take it somewhere. Also just incase you need it, he had the 88ci motor bored to a 96ci motor before he ever left the Harley dealership with it.

 

You probably need to replace the slow speed jet and adjust the idle mixture screw. A 46 or even a 48. You have to remove the float bowl on the carb. Read up on cv 40 carb adjust, jets and tuning.