Johnathon,
I have not ever tried to use a sine wave into this kind of tranny before. Remember it has very low impedance, as the magnetic circuit is rubbish. I am surprised the 3v dropped so small, I would have expected the primary to look like a short circuit of very few milliohms to your source transformer.
The trues wave form is a spike pretending to be up in the millions of hertz.... it has a very fast rise time to protect the innocent....
What exactly did the unit so when you fired it up, did it work then fail, are you getting the 600v in the cap, can you hear the oscillator.. I doubt the traqnsformer primary will fail.. it is fencing wire ...
What part of the fencer didn't work.
...................oztules