Very interesting reading for sure. I only made it to page 4 before I had to get back to work. I'm surprised that there are so many posters in there who understand the situation (obviously some EC's or POCO pros). There are still a lot of questions about the OP's story though.
My first thought was that the fault caused or escalated the failure of the transformer, where a winding shorted causing the output voltage to increase dramatically but not into thousands of volts.