1996 Geo Metro electrical issue

Starting out, I'd like to say it's 3 cylinders not 4, there was no option for 3. But I have an electrical issue that started shortly after going down a washboard like road, roundtrip, and having the headlights running for a short period of time while parked. The first signs were my CD player was turning off and then back on, it wouldn't reset the programmed things just off and then back on, but at first it would only do it higher volume levels gradually worked it's way down to lower ones until I had the CD player turned off entirely. After this my headlights dimmed down to almost nothing, my airbag light came on, pretty much any power accessories I had were gone in about a 2 hour time frame. When I got home and turned it off and tried to start it, it was immediately dead. First I figured it may have been my 800 watt amp with a 2 farad capacitor on it. So I disconnected the power from the battery terminal for the amp, removed the fuse, etc etc, but the problem still persisted. Before that I took the capacitor our to see if it was causing a back surge, but no luck. I then disconnected the CD player from the harness assuming that it had to be that. Again, same problems, the battery was just slowly dying. At this point I assumed it was a short somewhere because it ran for 2 hours in this "weakened" state so I thought it ok to rule out the alternator. I've gone through about 4 batteries now, each dying in about 3-4 days of 30 minute use, in total, per day. A battery charger I have, said the alternator was in fact bad so I bought a refurbished one for the Geo, everything seemed fine so I hooked the amp and cd player back up. For that day everything ran fine, no power loss in the cd player at higher levels, no loss of power or headlights, but today it started all over again. I have a very limited knowledge of electrical things lol, but no fuses have blown in all of this, and everything seems to gradual of a decline in the battery to be a short( in addition to checking the harnesses for arcs), the alternator is new, and what really stumped me was my capacitor read the battery voltage at the same number as the battery charger which is around 12 volts even after the problem, a little more when running, so what could cause the cd player to lose power at higher levels, then lower(over time), the car to gradually lose power, but still have the battery reading 12 volts from 2 different sources? Or is it possible the amp and capacitor are too big for the alternator and they burn it out, which leads to the gradual decline of the battery?