On newer roundys (like CTC-16 era) I've heard of folks having successfully removed the fly's HV winding and getting their HV from a solid state HV trippler the input of which being connected to the HO Tube's top cap....This may also be a solution for your CT-100.
Two options to further confirm your flyback is at fault are to compare it's winding resistances to those listed in the Sam's folder, and to get a vintage flyback/yoke ringer (aka a flyback tester) and see how yours tests.
Good luck fixing it.
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