2005 S60 -- Key remote and door module won't work after disc

[dfarthin]

I am replacing the factory head unit and speakers (and adding and amplifier for the speakers) with aftermarket products. I have been working on this project with my dad (engineer, but not a mechanic) the past few weekends. Before removing the factory head unit and doing all of the work, we disconnected the ground. In taking Crutchfield's advice, I was determined to run bigger speaker wire to each of the speakers. We needed to run the new speaker wire from the door into the car through the sealed hose in which all of the other cables from the door is ran. There is a "plug" connection at each door that does not allow wires to pass. For the back doors, we were able to tuck the speaker wires to the side of the plugs and into the car. No problems there. For the front, the situation was slightly more complicated given the seal around the plugs. Tucking to the side was not an option. We had to drill a small hole in the door and (carefully so NOT to damage wires) make a small slit in the hose and ran the speaker wire into the car that way. We sealed the holes we made with silicone and thought we had done a fine job. When we turned the car back on we had an error message that read something to the effect of "SRS Airbag alert". While I'm not sure what to do with this, this is not my primary concern. ALL of the doors except the front driver's side door has full functionality (this is where the main module is). Windows, locks, it all works fine for every other door. However, with the front driver's side door, there is no response when engaging any of the buttons (windows, locks, rear-view mirrors). Using a multi meter, we checked the connections in the driver's side door module and saw that there is 12 volts there, and we are confident we did not damage any cables when running the wire. Another relevant factor is that the lock/unlock functions on my car key will not work either. Is it possible that all of this is a software issue like the airbag? I realize there are several variables here, but assuming that we did not damage any of the wires, what could cause this to stop working? Surely this would not happen if my battery were to simply go dead from leaving the lights on or anything minor like that? Although it should be noted that the car ground was off of the battery for a week in between work sessions. I would GREATLY appreciate any advice/input at all! Thanks!