OK, reading through the thread, it seems to me that the MOSFET or the inductor is the culprit, and when the high voltage circuit starts to go wrong, it loads the power supply and this causes the 5V line to drop.
Once that happens, we no longer have the gate voltage to drive the MOSFET full on, and we go into meltdown.
I can think of three possible causes here:
1) The MOSFET has a high switch on voltage that the controller can't reach and this means that the FET stays partially in the linear region and heats up. Unfortunately, a hot MOSFET has a higher transition voltage than a cold one, and this has a runaway effect. More heat means worse switch on, means more heat.
2) The inductor is out of spec (<<100uH) and saturates, causing the MOSFET to short the supply, getting hot and running away.
3) The controller is either running below the required frequency, or has an unstable clock circuit. If the frequency drops, even temporarily, we go into 2)
At the end of the day, we have a "get you going" guarantee, and if you've had it with this board, let me know and I'll repair or replace it, giving you a fully assembled board if you want, or a kit, or a set of parts to substitute. Totally what works best for you is the best option for me.