I know on 89 and below, you don't have the check engine light problem.
On my 89, there are two plugs that go into the factory HU. They are for the speakers. You can see where the PO hacked into the blue and white plugs. There is another plug that is black, and that is for the antenna, dimmer, ignition, and ground:
Those 3 plugs plug into this factory wiring harness:
What I'm doing is I'm gonna plug the black plug back up to the wiring harness pictured above. Then I'm going to butt connect my speaker wires to the Alpine wiring harness that goes to the HU.
Do I also need to unplug the bose relay? I'm assuming you guys are calling it the radio rec? I'm thinking it's not doing anything, as I believe the radio sends a signal to it, and with that wire unplugged, the relay isn't doing anything. But I'm not sure, I just don't want any live wires.
And here's a pic of one of the rear bose pods. I'm removing it and using the factory mounting ring for 6x9's: