Good observation on the A6 card. Is there any signs of rework like soldering? Still it may or may not be bad. Clearly someone was careless with putting back all the hardware. Since all other bands work there is only a few places to evaluate that is unique to band-C.
Regarding degraded resistors: It's always possible although I'm sure HP used top shelf components. Generally I expect to see problems with electrolytic and semiconductors before drifting or failed fixed resistors. It's better to use measurements at a systems level to identify a problem subsystem first then start looking at individual components.
"YTX linearity adjustment circuit being wonky":
This subsystem is utilized by
all pre-filter bands B-E. If it "wonky" why doesn't band B,D,E exhibit the same drop in RF level? Does this theory really make sense? Shouldn't any subsystem shared by bands B-E should be low suspect? These other band are working correctly - right?
Get better characterization of the problem behavior:
1. Is the low amplitude points caused due to the pre-filtertuning too high or low? Both situations will cause a drop in RF level. How did you objectively establish that the YTX is actually tuned low rather than high? Is it consistent across the problem frequencies? You know you can manually control the pre-selector DAC with <SHIFT><=GHz + dBm dB>....you can see the RF signal level vary as you move through the 64 level range. At 12.1 GHz my system reads "33" which is about center of the range (which is probably ideal).
2. Did you figure out how the "PRESEL PEAK" ties in with the normal tuning? This is pivotal to troubleshooting this issue - don't you think?
3. How are you going to measure YTX tuning?
4. There are other diagnostic features on the system you could also leverage. For example: Band lock, DAC setting, Step Gain level, and LO setting.
Some Ref material:
http://www.siliconinvestigations.com/HPREP/HP8566-8/8566A-opr.pdfPage
58 Information on preselector peak values held in memory for each band.
86 Some diagnostic modes
89 Factory preselector setting; Manual preselector tracking. (Troubleshooting?)