Did you ever find a soultion? There were a few Kenwood units using this X08-3090-xx PC board. I have a VR-5090 and love it. I called the Kenwood parts suppliers in the U.S. I was told that Kenwood never offered this PC board as part of a spares kit. Board level troubleshooting is the only way to repair. Seems like your shop did not want to do that. I am having the same problem and will need to push them.
My receiver has no output on every mode except the Pro Logic settings. The problem is intermitent. What I found is that if I remove the power for a while and then put the unit into test (diagnostic) mode it would work properly. If I were to use the input selector or the DSP key on the remote, the receiver would return to Pro Logic only. Basically, if I used the receiver after a reset it started to not operate properly.
I suspect the CPU because it seems to be a control problem when using the input selector or DPS modes. The good news is the CPU is still for sale. The part numbers are in the service manual. Use Google to search for it.
You mentioned that output problems were common in the past. What problems are you aware of and where did you locate them?