Thankfully I am a tech and know all about high voltage step up transformers. Since my original post I have narrowed it down to the primary transformer. Because they use a custom handmade transformer which appears to utilize a multiple level step up design, I will need to know which pin in the connector is used for what. Since I could be looking for at least 600 volts, I know not to cross the wrong wires. This is why I first need to find out which pin does what and what value I should see at each pin.

Transformers are actually very simple and this one is no longer stepping up like it should, I am probably going to be looking for a replacement transformer. :-(