i have been following this thread and trying to develop a convenient way to troubleshoot.
here is my question,has anyone tried to eliminate both the compressor speed signal and the engine speed signal for the purpose of determining if the compressor would run in the auto mode?
has anyone got access to the internal drawings of the kilma relay?
in most cases ac signals are rectified and converted to a pure dc value for the comparator circuits. it sure would be convenient to eliminate this possibility when troubleshooting the system.
by the way some one asked about the signal level at n22 pin 1 from s31/1 and it is high when compressor is off and pulled to ground when on.
also i am working on a 88 300te,86 300e and both have the same problem,at times wont cycle back on when in the auto mode but will run continously in the manual mode.
larry perkins lou ky

Seems like a whole lot of diagnosis work here....has anything been replaced? I would work under the assumption, since the AC does work - all be it sporadically, that it is probably a broken solder connection in the CCU in the dash (the push button unit). My 87 560SL was doing the same thing your car is doing. Compressor would come on and then shut down, the fan would come on and then stop for no reason. It was maddening!
Replaced the CCU with a rebuilt one from Benz Barn our of Georgia for $135.....everything has worked great since - even got the vents to work again (was so afraid it was a heater box thing!).
Even if that part does not solve your problem it will take a big known problem component out of the diagnosis and get you some new shiney buttons!
Good luck!