The battery is there to keep the static RAM chip from dumping it's contents. Folks use flash memory for that sort of thing now but yes the back up battery being dead can make all sorts of things do crazy stuff so it's good practice to start there since they are so cheap to change.
After installing a new battery, I'd probably reload the software just to be sure you get a good clean start up.
I assume you've tried several patches and have disconnected the long board to simplify things.
BTW you don't really need a spectrum analyzer to signal trace the amp but a common oscilloscope would sure go a long way towards troubleshooting both the digital and analog stuff. Then again you'd have to be familar with this sort of thing, if not I'm sure you can find a friend who is.
BTW The service manual can be downloaded from the Internet at http://elektrotanya....f/download.html Ever who digs into it will need it. It's for the head amp but the head and the combo amps are almost identical in large part. Enough to nail your problem anyway.
Is there a common Achillies heel on these amps? Something that routinely fails?
Edit: After reading a few comments, I recall the seller telling me the battery might be suspect. Would that cause the output isssue?