My way would be;
Look for 12+ volts (12.0-12.5) at the battery and 13.5+ (13.5-14.5) when engine running at above charge point.
So to do that;
- hook up the multimeter to the positive and negative on the battery
- check voltage, should be 12 volts
- turn on the key, check voltage, should be 12 volts but may drop slightly, more if headlight is on
- start bike check voltage, should be 12 volts
- rev bike to about 2,500+ rpm check voltage, should be 13.5-14.5
If not you still have issues. Try another battery and repeat.
Above is standard test no matter what type of charging system used on the XS650.
Still issues, recheck regulator/rectifier and charge coils again.
In your case, coil check as stated by Hugh at connector using Ohms reading.
And follow with standard regulator checks.
Look for bad grounds.
Ground between engine and battery very important, because it is between the mounts and frame and ground lead the battery is attached to.
Jumper cable attached to bare metal engine part and negative battery terminal will help to determine if that is the issue.
You have painted everything, hope you bared some parts to make good metal to metal contact for the grounds.
Ground to reg/rec box important here as well.
Good luck.
