Another thing popped into my mind:
Before putting the transformer back, if you have another scope and a sine generator, you could verify the fase of the windings.
And another one:
Once you are at the point of powering on again, connect a voltmeter to the first switcher to check the 43V it is supposed to generate.
It could be the first time -because of the wrong feedback signal- the voltage of the first switcher was way to high, and the scope was saved by the second regulator and the crowbar circuit.