Overcharging problems
One question down.
A few more to go. LOL
Because its no longer stock, and we don't know know where things have been tied in, modified, or where the voltage is being measured.
There standard wiring scheme is like this

But cars with rear defrost, and maybe other options came with a heavy duty scheme.
See the link I posted earlier.
Shunt.
There's a recent thread where someone pointed out the downsides of using a shunt. There are upsides too. In any event, it may or may not have just made diagnosing more difficult because we have to either guess the current paths or you do some voltage and current measurements.
67Dart273's point about the regulator sensing a lower voltage remains valid. Take your finger and follow the path to the regulator;s sense terminal. The more current sharing that path, the more voltage loss.
change in Voltage = Resistance x Current.
The big high rated alt may or may not help at idle rpm. Those ratings are always at some high rpm.
One hting it most certainly will do is draw more current to created the magnetic field. So the wiring to the field needs to be up to that task. The regulator also needs to be up to that task. In my experience the MP P part VR does not due will with even the revised squareback's field current.
I'd start by ditching the electric fan. Put a more normal alternator on it, and then diagnose.
One last thought. Battery condition can effect the charging too. Dana recently had a thread about this.