Hmm, interesting. May be worth finding a similar picture of someone with an r3681 series instrument to see how the different synthesizer plugs into things there.
Since the 200MHz input is kindof an odd one..... could that be something not generated by the r3681 synthesizer board? If so maybe it's an external input needed to run properly? I wouldn't really expect it... but if you have the means of feeding a 200MHz signal into that input, it may be worth trying to see if it clears up the error. Perhaps whatever benefit going to the upgraded synthesizer gave (phase noise, sweep speed?) meant they had to get the 200MHz IF from an external source. Though I'd expect that to be locked to other stuff..... so I maybe there's not a big chance it relies on the external input. I guess in either case, since it was originally specified as an output, maybe check to see where it connects internally before applying a signal.
If you haven't done so already, maybe just mapping out the layout you have can help decipher it - seeing a sort of flow chart for the system could clear up how it's actually operating or what could be missing easier.