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Here's back story: starts with a BP Swap afterwards my battery would continually die. I replaced alternator belt, then bought new battery, then I realized the alternator I got with my swap was shot.

So I put a brand new 65A alternator in (wanted to use my old b6 70A alternator but The shaft for the pulley is bigger) and checked voltages and it seemed to work, but my battery kept dying.

Went to Advance auto and they replaced my battery which was an Optima less than 2mo old and Checked my charging system. the read out said that my charging system has low voltage. My system with no load was 14.26v and under load with high beams and heater full blast was 12.08v.

What could bee the problem, is it possible that my old optima dying out so many times due to my old alternator not working destroyed my battery and it wouldn't charge? Could it be something in my car drawing to much power? Could it be wiring or grounds? I checked wiring and grounds previously and everything checked out fine... Also of note my car has aftermarket sub amp cap and head unit And i drive my car very rarely now since i work and live in nyc (it sits a lot in CT buy my family starts it weekly. Any ideas?

If it's going dead while sitting there, there has to be a drain somewhere, especially since you have a brand new battery. I'd take a good look at the wiring for the amp and cap. Make sure your amp isn't trying to stay on all the time, maybe the remote on wire for the amp is a constant on instead of switched from the stereo (this would be my first guess, and newer stereos can be tricky on that source wire, due to newer car technology). I still haven't messed with a cap, but it'd be a good idea to double-check that as well.
If the above checks out, recheck your wiring. It'd be a good idea to disconnect the battery when it's sitting for long periods of time. If the battery is being constantly drained, it can mess up the battery, but it shouldn't mess anything else up.

Yea I will check and see if the problem still occurs, good idea to take negative batt terminal of I was just hoping to solve this problem all together and not have to worry about batt dying again. I'll look into my stereo wiring, its just weird because I never seemed to have that problem before and no new wiring has taken place since my swap... still possible though.