I didn't use any of the spacers when I installed the R4 in my grey 300SD. I remember one seal was thicker than the other. You want the manifold to fit on the compressor flush with the ports and you should be able to test a few different seals before you tighten it down. Green and yellow should work. I am assuming the one without paint on it is the yellow one.

I also bought the R134a conversion seal kit to replace all the O-rings in the system. You can run R12 on those seals, as well.

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1991 F250 super-cab 7.3 IDI. (rebuilt by me) Banks Sidewinder turbo, hydroboost brakes, new IP and injectors.
2003 S430 - 107K
1983 300SD - Tanoshii - mostly restored ~400K+.
1983 300SD - Good interior. Engine finally tamed ~250K.
Monark Nozzle Install Video - http://tinyurl.com/ptd2tge