I know how systems work. Any OTHER suggestions?!
How about CANBUS? I don't know enough details from what you've posted to have a good idea about what's going on, but from what you've stated, it sounds like the modification itself is the problem. Members with at least 2 or more years presence here on the forum can recall a number of problems associated with stereo upgrade attempts, so the recommendation to set it back to stock does not originate from a quitters attitude. It's difficult upgrading to a higher option status using original equipment from a donor car as a result of the sophistication that comes along with the high-tech.
Is the battery being drained as the car sits parked overnight, or is it drained after driving for a while, then shutting down and stepping out of the car for a few minutes and returning to continue? That's an important difference not made clear here.
I can't imagine and am pretty sure it wouldn't happen, that you could drive along with insufficient voltage/current supply (due to stereo load, or any other) and no trouble sign be given in the form of a chime, or the notorious loss of power steering that almost every single alternator failure is accompanied by, with insufficient voltage in this car .
Are you aware of the fact that the computer controls the alternator output and determines the voltage output under all conditions while the motor is running?
Have someone with a capable scanner check the car for body control module codes (BCM) and see if you have any, chances are you do and they do not set off a check engine light. Codes of this nature can offer clues.
The CANBUS system is the internet highway for the car and it is used to transfer and receive data between modules (all onboard computers), that can cause problems like this when the information depended upon is missing, or in error.