Sorry you had to wait so long for an answer. It sounded familiar to me so I went searching. Didn't find a final answer, but I found the familiar thread:
zerothread?id=157937
My guess is a short somewhere. That would explain your dead battery, too. Time to dig out the multimeter - test all the fuses (they can "look good" and not be good) and check for any power drain. Are the old Bose amps completely out of the system? All you did was to unplug the harness from the aftermarket HU and plug it into the Bose HU?
Odd that most of it went away when you changed the battery.
Modified by 96Qowner at 11:26 AM 7/6/2007