New charging problem

I'm not running any capacitors on the stereo, it's not that big of a system.

The troubleshooting has been done both with the stereo on, and with it completely unplugged. No change between the two states.

Ok, that rules that out.

I am using all 1/0 cable for the battery cables and 4awg cable for the charging wire. There is very little voltage drop from the alternator to the battery.

Currently I feel there is something else amiss in the vehicle and throwing a new alternator at it won't solve anything.

I think your right that a new alternator won't solve the problem. Wish I had more to offer though but it sounds like you've been around the block on it. The only thing you might try is to remove the remote sense wire and wire it up like it was from the factory. I'm sure that should lower the voltage some.