Carb problem or electrical
Just adjust the idle mixture screw until you get the maximum RPM out of it at idle and give it a try.
The choke being used too long indicates too lean of a pilot jet or whatever circuit they are called on your Harley. The hesitation in the midrange could be too lean in the needle or needle jet, try raising the needle first. Again my carb tuning experience is based on Mikunis and a few similar types, so just google your carb and you should be able to find diagrams and tuning recommendations.
Carb tuning is more throttle position related than engine RPMs. I used to put a piece of tape on the grip and another next to it on the housing with markings for 1/4, 1/2, 3/4 and full. I'd just check the problem against the throttle position to determine what jets were affecting the hesitation or bog.
Does the bike run okay higher than 3,000? If so your ignition is probably fine.
Start randomly adjusting the carb and you may have issues only a repair shop can straighten out.



