I'm sorry to hear that you're having trouble with that HV XFMR....
I did a lot of testing and evaluation for Bill Schell over the years and I don't remember him every testing a transformer with any epoxy in it at all. He and I both felt that we oughta get as far away from that as possible. He first wound them without sealing them and I have never had one of those fail. Then when he started treating them with beeswax and a vacuum chamber, it seemed like he had found quite a good process. So far, I have never had one of his fail, of any description.
Just saw your later post and I'm glad that yours is improving! A friend of mine has restored an original xfmr by putting it in a vacuum chamber and keeping it in a deep vacuum for a while. Don't remember how long he left it in there.
I hope yours comes out alright. It really does seem like the moisture is the major factor.