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Maybe there's a little too much current thru the flyback? That could melt some wax. And make for excessive HV? IIRC backing off on the drive may help, but the service notes should say what the current should be set to. I think you don't have a short in the flyback, or else the set wouldn't work as well as we see in the pictures, unless it got bad after the arcing. Some RTV should help, overcoating the existing wax "tire" on the high voltage secondary. But I'd check for carbon traces that may have formed in the wax.
Oh, I'm sure you cleaned inside there, so cobwebs and such should be gone.
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