2006 harley dyna charging at low speed, not at high rpms

This used to be a common problem back in the days of generators but I've not heard of this since Harley went to the alternator systems in 1970. It is unusual to say the least.

The first thing I'd do is have my battery tested. This is simply good procedure anytime you are experiencing a charging system problem.

Next, check the output of your alternator. To do this, you'll need a DVOM, digital volt ohm meter. Unplug the voltage regular at the front of your engine case close to the oil filter. Now, put your DVOM into "Voltage", "AC", Range 50 volts or better. Now, with the engine running, put one lead from the meter to one of the pins in the plug in the engine case. Put the other lead in the other pin. Rev the engine up to about 2000-2500 RPM. You should read at least 30 Volts AC. You must have the meter in the AC positon because an alternator puts out alternating current. Your regulator converts it to Direct Current voltage for the charging the battery and reduces the voltage. If you are reading thirty volts or better, I would suspect the Voltage Regulator is your problem.