Start by checking the ESR of all axial electrolytics on all of the plug-in boards. 95+% chance that you'll find a few bad ones, hopefully one of them will make the 40 MHz artifact go away when you replace it.
The next thing I'd do, after replacing the trimpot you already know is bad (or bridging it with a resistor to force the adjustment point away from the bad spot), is to go through the calibration procedure and see how far you get. If and when you reach a step you can't complete, you can focus your troubleshooting effort on that particular section. Lather, rinse, repeat until the whole thing works.
You may need to get creative with test equipment substitution, of course, since many of the specific instruments they expect you to use won't be available. This is rarely a showstopper.