2006 1200XL custom changed voltage regulator, checked wiring to starter and fuses. still get low voltage code. what else could be causing low charging?

 

Could be a stator, however my wife's bike was getting a low voltage "code" and it turned out to be a stripped bolt hole on the battery terminal.

 

You should post your query in the correct forum to get more answers.

 

First how about getting a DMM and tracing down where the voltage loss is located instead of just throwing parts at it???

Throwing parts at a problem never the right solution unless the problem is obvious.

The Factory Service Manual will have a procedure on how to check your charging system.
If you are going to be doing the work on your own bike then it is an essential thing to have.

 

If you're checking the voltage at the battery you have a discharged and probably bad battery, it's that simple! The minimum voltage that can show would be what the battery has left in it. Test the battery independent (disconnected) of the system and then make sure that the battery connections are all tight and clean at both ends of the cables, to test the system.