Ok. So I have done a little more testing. The battery drain does not occur while the car is off. The battery drain occurs while the car is running, rather, from the car running. The problem IS that the charging system is not working.

I went to the junkyard today and salvaged some wiring off of a 90'. I replaced the janky (but for 5 years functional) grounding on the alternator and fixed a loose ground from the negative terminal - one goes to the frame one the engine. The one on the engine was about to fall off. My repair on the positive charging line running under the engine held up (the one mentioned above). Still having some troubles with it charging though.

For some reason, it does not want to charge running through the alternator charge line fuse box - a small single 25amp fuse. Connected directly to the battery, its fine. Not really sure what's up with that, fuse is good, connectors clean.

I did find a bad ground today, and I'm thinking that may have ruined the warranty replacement alternator. I'm about to take it over to autozone and have it tested and maybe replaced.

Any other ideas as to why the charging system is not working would be welcome.