OK first off I'm a mechanic at a shop with access to all the things. Customer brought in a 2002 XKR that had been sitting for years. Battery was dead but when jumped would start and everything worked fine. New battery put in and then next day would not start. Removed the BCM and disconnected the battery overnight and then it was able to run and drive. However now about half of the electronics are inoperable. Here's a list of stuff that stopped working:
1. Convertible top (Rear quarter windows don't roll down, switch does nothing)
2. Electronic Mirrors
3. Trunk release, inside and outside
4. Cant program Just the Passenger Window, Drivers is fine
5. Gas Tank lid release
6. Electronic Door locks, will manually lock and when unlocked via the key it will cycle 3 times lock unlock etc and then remain unlocked
7. Keyless Remotes, Security Light does not illuminate and i cannot program remotes
8. Valet Button does nothing, was thinking maybe valet mode was active, no luck
9. The siren under the from bumper will not chirp and when the car is knocked it sounds like a dead cat, so maybe an alarm system issue?

So I checked all the fuses and relays etc and they are good, tried a hard reset, and a new BCM with no luck. I can read the BCM but when i try to clear the codes it crashes the scanner which is why I thought BCM. The only codes I have now and did originally are: B1595 Invalid Key input that comes and goes, and the ones for the steering wheel adjustment motors. don't have the number on hand but if i turn off the auto adjust steering wheel they don't come back. And Finally an ABS can bus comm code which is most likely from not having the vin programmed, it wasn't on the first BCM only came up when i tried the new(Junkyard BCM)

Now from here, i would like to know if anyone has had or knows a good place to start troubleshooting from here, I haven't yet programmed the new BCM so would the programming effect these issues but still allow the car to start? Could it be an issue with the security module?

 

So update to this issue. Looks like it was just a coincidence with the problems and battery swap. Opened up the SLCM and looked like a smurf took a dump inside, corrosion everywhere. About 30min some flux and solder, and alcohol and we were back in business. Cleaned up all the corrosion with a brush and alcohol reflowed the connector solder joints, the mosfets, the 80pin IC and all other misc IC's and Caps that looked suspect. Popped it back in and most stuff is back. I still have no gas lid release and power mirrors though.