Scope has been working fine this past week provided that I remove AC power when I am done for the day.
I decided to take the covers off again and add test wires to +5VSB. +1.5V and add a 10 pin ribbon cable and IDC connector to J9201. I ran the test wires through holes in the metal covers and out one of the narrow cover slits on the case back cover. I added another 10 pin IDC connector after passing the ribbon cable through the case back cover.
I checked J9201 for ground connections before closing the covers and pins 2 and 10 are connected to ground.
Before connecting the AC power and turning on the scope I connected a logic analyzer (Intronix LogicPort) to the ribbon cable and manually triggered it as I pressed the power on button. As expected, the scope powered up as AC had been removed for a long period of time.
I was able to verify that even when the scope is completely operational, +1.5V test pin indicates 0V. Must not be needed with my version of the MD4000 series.
The logic analyzer did not capture anything of value except for occasional narrow pulses on pin 3 of J9201. I put a meter on that pin and it read about 1V with the logic analyzer connected and 0V with the logic analyzer removed. All the other signal pins were at 3.3V with or without the logic analyzer connected so they must all be outputs. There was probably enough noise on the signal to fool the logic analyzer into thinking pulses were present.
I connected 3.3V from a lab power supply through a 10K resistor to J9201 pin 3 thinking that this pin might be used for external connection detection. I powered on the scope again (AC had not been removed) and I expected the scope to fail. I triggered the logic analyzer on one of the other J9201 pins that goes to 3.3V at power on. Much to my surprise, the scope powered up completely. This time the logic analyzer captured data with pulses detected on J9201 pins 1, 4, 5, 8 and 9. None of the pulses looked like a clock. It is not yet clear to me how these 5 signal lines are being used.
If anyone is interested in seeing the logic analyzer output, send me a PM and I will forward the file. To view the file you must install the LogicPort application and run it in DEMO mode. Everything works in this mode with the exception of capturing data since no hardware is present.
Now the stranger thing. The scope has powered up fine every time I tried if for the last 2 days without removing AC. There is nothing connected to any of the test wires I added. It is possible that this is a connector problem (but I don't yet understand why removing AC power fixed things). There is a logic board on the back cover that contains all of the rear connectors, the clock battery and the two front USB jacks. The logic board has a card edge connector that plugs into what looks like a PCI socket on the main board. Possibly the multiple removal and insertions of this connector wiped the pins enough to clean the connections. This scope is almost 8 years old and last week was the first time I have ever opened the scope.
Update
I found a service manual for the MDO4000 series scopes, J9201 is listed as a JTAG port.