I'd first suspect a bad HV rect or more likely a short in the HV wiring (say the HV filament winding or another place it gets close to grounded metal) or excessive load from a miss-biased or gassy CRT or HV regulator tube.
Good diagnostic methods: disconnect the top cap from the HV rectifier and see if you can draw an arc 1/4"+ from the top cap lead or fly doughnut with an ungrounded screwdriver...If yes your fly and its drive circuits are fine. If you have a neon bulb or CFL you can hold it near the fly and H output tube and the ambient RF emitted by a good horizontal system will light the bulb.
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