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D109 is really just a short term fail safe (if the regulator loses control of the 3V supply. It shouldn't get activated unless there's a problem somewhere else (like a short to the +12 supply...)

If it's toast, there was undoubtably a problem but where? :-(

Paul -- AI7JR

You might check D109 (the 3V6zener on the #2 plug-in board. Mine was "soft" and although it began conducting a bit below 3.6 volts, it allowed the voltage to climb above 5 volts and caused a hard short to ground within my MCU pretty much like yours.
This is for my curiosity only. I haven't seen any offers of a loaded CPU yet and the replacement would be difficult even if it were.
At this juncture it might be best to order a new kit and start over. If you do then you might check D109 before applying power just to make sure. Couldn't hurt.
Please keep us posted if you find out more.
-Don-

-- 
Paul -- AI7JR