Here's a couple of ideas that might aid in troubleshooting. Bear in mind that I have never built or even seen a Megatron.
Milos - Despite the obvious damage to your supply board, you probably have the easier task. Almost certainly you have a wiring error, solder bridge, or reversed component.
Do you have an actual burned spot on the board? Which supply (pos. HV rail, neg. HV rail, low voltage ) actually blew up? If nothing at all works, then you need to look at the early part of the circuitry where there are common elements to all supplies. If only one supply blew up, I would disconnect it and retest the other supplies for normal operation. Once you've got it isolated to a particular supply, inspect each and every component for proper value, polarity, position, and physical integrity. You will probably find something like a reversed electrolytic cap, a wrong valued resistor ( I still sometimes misread color codes), or a backwards TO-220 component. If the board is damaged (broken trace), you will have to solder a wire bridge, or if the damage is too severe, then junk it and start over. Besides a minor repair of the board, I would not reuse any of the components in the blown supply. If you are able to repair the board, check and recheck the value and polarity of the new components as you install them. Keep in mind that the HV rails are mirrored and not identical. In each supply,measure the resistance to ground at each junction in the current path all the way to the output. If you have a zero or near zero at any point, you have a problem. If in the end, if you can't find anything, build another board. When building any circuit board based project, unless you are very familiar with the circuit, one should always have extra boards.
Enrique - You have the tougher task because it is intermittent. Next time the amp starts humming, try tapping the top of the case with a small dowel or unsharpened pencil in the area of the suspect 12AU7 ( are you sure the hum originates there and not earlier or later in the circuit?). If you can make the hum change by tapping in a particular area, then you probably have an intermittent connection at some nearby point. Reflow all nearby solder connections. Redo all your screwed terminal block connections. If this doesn't do it, try running the amp with an oscilloscope connected at different points in the signal path. If nothing works, rebuild this part of the circuit with all new components. I've had a problem similar to yours that was caused by a nine pin tube socket that wasn't perfectly soldered to the underlying board. It was the last thing I was looking for and took me way too long to find it. The socket and board were brand new. Everything looked and measured fine. For lack of anything else to do, I finally replaced the socket. Problem solved.
Hopefully someone who knows more about this particular amp than I will chime in. Or at the very least add some more general troubleshooting tips. If anything I have said here is incorrect or inapplicable, then please correct it.