All points measured at U3.
-15V rail: -16.5Vdc w/ 65mV ripple
5V rail: 5.5Vdc w/ 65mV ripple
15V rail: 16.8Vdc w/ 70mV ripple
CR20: 6.3Vdc w/ 58mV ripple
While trying to figure out where C16 was, I realized the board layout in the manual I linked above is slightly different from the board I have. I found an updated
manual on Fluke's site that matches my board.
I ran through the flowchart and ended up at "Check Period, VCO, and CR20." CR20 and VCO check out fine. It's just the measurement period that is off. In a fit of madness, I removed and verified R20 (period adjustment pot) and R56. R56's value isn't specified in the manual. Mine is a MIL spec 442k 1% part which seems a bit odd as none of the other components are MIL spec.
Looking at the pieces of the matched set (U3, C14, C16, CR20, R56, R57, R58), they seem to be part of both the VCO and the timing control which are both part of U3. I can't find any indication that the VCO's operation is related to the timing control though. Pin 5 of U3, where C16 connects, shows the same frequency as the VCO test point (TP1).
If the VCO and timing control are independent, then the period should only be affected by U3, R20, R56, and C14. I don't own an LCR meter so I checked C14 with my Fluke 87 which doesn't report ESR. That could be an issue though I'm starting to suspect that R56 was replaced with the wrong value at some point.