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Well, I figured out what I had done wrong with the soundgate install. Apparently the amplifiers for the Bose door subs are tied into the power antenna lead on the soundgate, so hooking that up to the antenna lead (and not the amp turn on) of the deck made them not fire unless I was listening to the radio.
So, I fixed that, and the system sounds 100x better with some bass coming out of the front of the car.
Now the new problem: I'd rather go back to having the antenna only go up when the radio is on. Does anyone know how to split the actual antenna wire out of a soundgate hookup so that I can wire it back to the Head Unit's Antenna-on wire? It seems a bit odd that they just cut corners like that.
The alpine head unit does have both an amp on wire, and a power antenna up wire, but the soundgate harness requires it's antenna wire to be connected to the head unit's amp on wire so that the door amplifiers turn on. (the side effect is that the antenna always goes up when the radio turns on).