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.
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.