Oh I can tell you some horror stories about charging system tail chasing. I think, if you put on a new unit, you will still have the same readings. It sounds like you are familiar with the alt, or you wouldn't have tried the rebuild. I think that you may have a degraded ground (bad neg bat cable). To check this is not too hard. I assume that you have a multimeter? With the car running and maybe the headlights on, measure the voltage drop across the neg bat cable. In other words, set the meter for dc volts and put one lead at each end of the neg bat cable. Don't worry about reading pos or neg volts, it doesn't matter. You shouldn't get anything more than .1 or .2 volts. The same can be done for the pos batt cable for that matter. The point is is that there is a series resistance that is causing a voltage drop.
I had one that started fine, all of the accessories worked well, power windows were fast, ect... but the voltage read across the batt was 13.2 volts. Checked the battery cables, using the ohms mode, and had 0 resistance. When I ran the car and checked the cable (neg) with the volts mode I had a one (1) volt drop. Replaced cable and wellah 14.2 and better running accessories.