What is your temperature gauge showing, is it getting up to normal temperature, or is it staying barely off cold?
If the thermostat is stuck open, the engine stays cold, the glow rail controller keeps the glow plugs turned on due to the low engine temperature, especially during winter, with lower air temperature, more use of lights, defrost, etc, the alternater can't keep up with the draw off, due to the glow rail staying on. Altinater is charging, but battery still goes flat occasionally.
Wasted money on battery and altinater replacements, before I cottoned on to this, I initially found the glow rail stayed live (volt meter) and thought the relay was at fault, but the engine was not getting above 50 deg C. It would charge, after parking (at idle) due to heat soak increasing the engine temperature after a trip.
So this can easily be a non electrical fault, which presents as a very electrical symptom!

 

Temp gauge reads fine, and it gets up to temp with no troubles. And when I short the field to ground on the alternator, it charges just fine, just can't seem to get it to charge on it's own, time to have the regulator tested somewhere or just replace it again, at least it's only $15. Thanks again for all the help guys, and I'm getting voltage over to the alternator, but I think the PO kinda hotwired the 12V over to there. Does anyone know what voltage the alternator and/or regulator are supposed to see to function properly?

 

So I tried another voltage regulator and the old girl charges again. Go figure. But it still does kind of a weird thing while charging, the voltage needle swings back and forth when the RPMs are higher than idle, is this normal? I'll try to take the camera with me later today and post a vid of what it's doing. But the good news is that it's charging again.