2 other places to look-
First, the alternator can do that in one of their many failure modes. Try unhooking the alternator and see if it still drains.
I too agree that the stereo install is a likely culprit. Try isolating components one at a time instead of all at once like you did.
One other oddball thing to look for- the trunk light is shutting off, right? Any chance you bumped it while in the trunk for the stereo install, and now the mercury switch isn't shutting off?