The previous owner of my '06 obviously had an amp and sub in the trunk -- still a power and ground in the spare area and there are 4 wires also in the spare area that are cut and run to the back of the Bose unit in the RR fender well. Additionally my stock sub controls do not impact sound at all -- apparently it's disconnected.

Any obvious plugs or wires to check to see if the stock Bose is hooked up? I have a feeling I'll need a dealer to check this out, yet thought I'd ask.

I finally had the time to track down the tvnav2go unit in the trunk -- that set-up works sweet now that I figured out where everything is at.

 

Sounds like those 4 wires were probably ran to the LOC for signal to run to the aftermarket amplifier. Follow the wires to the obvious cuts im sure it should be pretty easy from that point. Also if this was done chances are that the rear mic behind the rear dome light is disconnected as well or they would have ran into many problems without doing this as others have in the past. Look for this as well and plug the mic back in.