Andy,
my idea is: electronics

what you describe in how you can get stability after (auto)focussing for a few hours, then degradation, sudden or slow, is what we saw a year ago on an old conflo Delta. We suspected a source electronic problem. Thermo came and did some tests, then agreed to try switching the electronics even if they were not convinced it was the problem. In the end, the instrument behaved normally. I can't be completely sure this was the solution since our observations of the problem weren't as detailed as yours and we and Thermo did a lot of cleaning and testing and changing the board in a short time, so it's possible it was another issue. But maybe it's something to check next.

That old electronics would behave like this makes intuitive sense to me. You set up a new voltage for one of the source parameters, it can be held for sometime, then it fails and goes to another value, loosing the focus.

Julien