I really try to stay out the threads that I'm not pretty darn sure about and try to avoid the 'have you tried this or that'. My major experience is limited to my 560sl. I've found that the Sl and SEL do share a lot of common parts and design aspects. I may be way off base but I admire your effort and will weigh in with my two bits.
This is only known to apply to the SL, I only THINK it applies here.

The ONLY electical connection in the door that is associated with the central lock system is the switch that is part of the vacuum actuator.

The wire group that connects to the actuator is red/blu/brn

There is another 'mystery' pair grn/yel on the LF whi on the RF. This pair sits in a black plastic holder that is outboard the latch on the door jamb. The wiring diagram seems to indicate an 'alarm bypass'. On mine this is connected to nothing. When this plug got crushed on mine (door closed on it) the alarm triggered.

!!!!!!!! Now my lesson learned after hours of frustration !!!!!!!!

The door MUST be closed or the latch catch pressed over as though it's closed for the key lock to trigger the others

!!!!!!!! Constantly have to keep telling myself to KISS with this car !!!!!!!!

Yeah, okay...
So the only problem was that the repair shop had swapped the wire harnesses. In my frustration I turned a simple 20 minute job into over an hour of confusion. Anyway, everything works fine now and I can finally close this chapter. Thanks to Dokta and everyone else for the help!