break80,
It sure seems like nobody is reading all your symptoms!!
Let me just reiterate what you posted originally:
#1 remote keys only works to open trunk, but not on doors or alarm, although, still can use key to lock/unlock manually via keyhole, start engine, and truck runs fine
#2 Main cabin lights are out
#3 center console lock/unlock button unresponsive
#4 fuel lid locks/unlocks with the doors.
For #1, if the key works to open the trunk it obviously doesn't need to be sync'd to the car so don't bother doing the key sync procedure. #2, no interior lights is interesting. These lights are controlled by the body control module (GM3) and not the light control module (LCM). A bad center console door lock/hazard button would explain #3, but, not any of the other symptoms. I repair GM5 modules used in the E46 3-series and get calls all the time from people wanting to know if I repair GM3 modules because they have problems exactly as you describe, mainly door locks and interior lights failed at the same time with no bad fuses and have been told by the dealer that the GM3 module is bad and needs to be replaced. The quotes I have been hearing are in the neighborhood of $1K including installation and coding. Unfortunately I have not been able to get my hands on a bad module to work on and don't have a fix, YET! I'm determined to come up with a fix though. Your best option at this point is to order a new uncoded GM3 module from getbmwparts.com ($368.66) or ECStuning.com ($434.28) and install it yourself. But since it is uncoded you will need to take it to the dealer and have it coded which will run between $100-$150. The module is located behind the glove box and is a white box about the size of a VHS tape with three large connectors plugged into in. I don't recommend a used GM3 module because there are a ton of different part number floating around with different capabilities from multiple redesigns. I have noticed 6 major groups of modules and have noted them on my web site.
http://bmwgm5.com/GM3_Part_Numbers.htm When you go to order a new module you will need to give them the part number of your current module or the production date of your car. Depending on the production date it should be 61359117101 (up to 10/2003) or 61359117102 (from 10/2003). More general information on the GM3 can be found here
http://bmwgm5.com/GM3.htm
If you have a bad GM3 module with door lock and interior light problems that you would like to get rid of let me know, I'd love to have it. My email is on my web site.