Sounds like you need one of John's transformers, shoot him an email. RE low HV: disconnect the shunt regulator (6BD4), see if HV pops back up. The HV pot may be bad, do some futzing with the shunt circuitry, I wouldn't be surprised if you locate the fault. I've never seen a CT-100 flyback go bad, they seem to be better made than the later stuff. The outer winding getting hot tells me it's trying to put out the voltage, but it's getting lost to ground somewhere between there and the CRT.
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