IMO checking unloaded voltage from the yellow stator leads isn't a tell all. You could still have the mag slipping on the crank and or the magnet itself has come loose and is chattering around etc. I've seen some bikes with a worn crank bearing that walked around a bit and gave some funky readings.
Standard checks are to unplug stator connector. Check plug for yellowing or melting from heat. Check each leg for continuity to ground. Should be an open. Check all three to each other for resistance. lead 1 to 2 then 1 to 3 then 2 to 3 etc. Should have minimal resistance.
Reg/rectifier- Unplug all leads. Check, if your meter has a diode selector the better, for continuity from green thru each yellow, then reverse the polarity of the meter leads. Check red thru each yellow then reverse. You'll see basically that you'll get "opens" one way and the other resistance. Readings results itself, IMO, isn't as important as all readings being in "the ball park" with each other. You'll pick up a pattern.
I'd then pull the mag making sure bolt was tight and there was no sloopiness in the bearing etc Check crank surface and mag interlocking surface. See if any of the magnets have broken etc. Be sure stator plate screws are tight and there are no discolored windings.
The first thing I always do when checking a charging system is start bike and unhook negative battery cable WHILE hooking up my amp meter in series. Don't hook your meter up in series and use the electric starter. Your meter will go up in a poof of smoke. This can be tricky because battery powered ignitions will stall and you can easily fry your meter too. I have seen systems that would put out normal voltage but produce low amps under loads.
One other thing to consider- how is the air flow over your reg/rec? I see some fellas we custom XS650 that hide them in fake oil bags etc They do get hot.
TYPICALLY, if you're getting less than battery voltage out of the rec/reg you're probably have a broken keyway, loose mag, loose stator etc
