OK - here we go - these responses assume that the pins on the X11 plug are the same on your car as on mine ('92 300SE, which is also LH-SFI).

Pin 7 - this is for the Electronic Accelerator control. Code 6 indicates something wrong with the Starter Lockout/Backup Lamp Switch. I'm not positive about this one, as the #'s in the DTC (diagnostic trouble code charts) are usually identical for the impluse counter tool, and the MB-specific hand-held tester (HHT) - but for this system, the answers are different. Code 6 for an impluse counter tool, which I assume is what you used to pull the code, when I activate the link to go to the diagnostic steps, takes me to diagnosis for the cruise-control module.

Pin 16 - this is for the HVAC (Climate) control. You can also pull these same codes from inside the car at the CC unit. PM me if you want instructions on how to do this (makes pulling codes a LOT easier than counting 91 flashes). 91 indicates something with the Switch Cirucuit Ground Activation for A/C compressor. Diagnosis points to wiring, the Base Module (Pin 2 on X/11) or the Diagnostic Module Pin 19. Try pulling codes from those pins and see what turns up.

Pin 23 - this is for the Anti-Theft Alarm (ATA). Code 5 indicates that the last time the alarm was tripped, the source of the trip signal was either the left or right front doors being opened.

As for your other issues:
Passenger Rear headrest - if playing with the switch gets it to work, then likely the trouble is with the switch. To tell for sure, you'll need to gain access to the motor and see if it's attempting to run when you toggle the switch. Possibly you can hold on to the headrest to detect the motor "trying" to work? This may or may-not be helpful. The switches are uber-complicated - nothing as simple as 12v+ to one pin for up and 12v+ to another for down. The switches work in concert with a computerized control unit, so the only sure-fire test is to swap the switch for a known good unit. The switches are easy to remove - and easy to break if you don't know the trick. PM me if you want details. If I remember correctly, the switches aren't swappable Left-to-Right, so that probably won't help.

IRRC not working on Passenger door. I believe the sensors are the same left & right, and I also think the handles are easily removed without taking the inner door panel off, so maybe you can test by swapping the sensor from the driver's door.

If the door locks cycle on their own, you've got a sticky switch somewhere. I'll bet your door lock switch is on the dash - if so, disconnect the plug from the back (getting at this sucker isn't easy either). If the switch is in the door, also not easy to get at - requires removing the door panel. The pump under the seat is what makes the locks work. Try pulling codes from pin 20 on the X/11 connector to see what it tells you.

Auto window feature - this is a separate module from the ATA. Pull codes from pin 21 on the X/11 connector. This module is fussy - voltage has to be just so to get it to work right. My car auto windows work fine from the switches, but will only roll up windows when I arm the alarm. On occasion, I can get them to roll down when I disarm the alarm, but that's rare. You do know that the windows must be "synched" to get the auto feature to work, right?

IIRC lights should show Green for disarm and red (amber when things get old and faded) for arm.

Flat spot - what gear, and what RPM? This may be electronic accelerator issues. Someone with more knowledge on the codes for that system may have more insight.

Jake brake sound - no insight here.

Hard shift - from what gear to what gear. I'd guess 3 to 4 based on that speed. If the engine isn't running right, the tranny is going to get bad signals. Make sure that the bowden cable to the transmission is adjsuted properly and that the modulator on the transmission (black or grey cover on the driver's side above the pan lip, I think) isn't cracked or leaking fluid and that the hose that feeds the modulator has good vaccuum signal from the engine.

SRS light behavior is normal - that's what my car does too. SRS is first to light and first to go out.

With a car that is new-to-you, sometimes it might be easier with some systems to clear the codes and see if they return. The system will store codes that are transient, which can lead you on a wild goose-chase if the problem was only momentary at some point in the past.

Keep at it - these cars are amazing when they run right.