This is the second time I have had power issues with my instrument and the fix comes in the form of opening up the big box that sits behind the console and (very carefully) poking around to discover the problem. Attached are pictures from the diagnostic light/fuse panel on the top of all the power supplies in the box. As you can see on the second panel that lights PD281, PD321, and PD341 are off but the fuses are still good. These lights correspond to the individual power supplies (10-1, 12-1, 12-2) which are the 13v supplies for the objective lenses. Thankfully this time the power supplies were still functional but the connector from those supplies to the lenses had come lose. I suspect it may not have been plugged in fully at the factory and managed to work itself loose over the past 4 years. Plugging that connector back in fully brought the power back to the lenses and thankfully my e-beam reappeared.
OK, I am officially impressed with your trouble shooting skills!
We had a similar problem last weekend when I tried to fire up the Thermo EDS system, but it would not connect to the Thermo hardware. After re-powering the Thermo electronics and getting the same result, I mentioned it to our in-house instrument engineer (Steve Wiemholt) and he discovered (after poking around about as you did!), that the network cable had just barely pulled out of the CAT5 socket, because (as Steve explained to me), the cable had apparently been under tension for years and finally gave up last weekend. So he just pushed the connector back in (after giving the cable some slack) and the Thermo software connected right up!
"Fighting entropy one day at a time" is my instrumentalist's slogan...