I had a chance to look over your link and I have to say thats a very nice writeup!
Relating to using the MOV transformers as chokes I don't think you will have any problems using them as is in a stock configuration being that you are pushing many KV through them at only a few tens of milliamps.
So in a way you can sort of think of them as being like a 1000 ohm resistor. At 120 volts it would only let through about .120 amps but when pushing only 30 - 60 ma that 1000 ohms then only produces a 30 - 60 volt drop at 60 Hz which means that when loosing 60 volts off of a multi KV source the parasitic losses really doesn't add up to enough to concern yourself with considering the healthy level of HF blocking they will provide.
My main concern with them would be possible HV flash overs from the coils to the cores.