Think of it this way, you have two outputs of the xformer, they go into the low pass filters (One filter per output), the output of the low pass filter will go into the safety gaps. The safety gaps go to tank. If you get a HV kickback the safety gap will catch it before low pass. The low pass removes the HF RF. The HF RF without low pass will focus on the first few windings of the secondary and will start to break down the insulation. Setting the safety gap is easy, just move the gaps togeather to they start to arc without the tank. This is the output of the xfomer max rating. Then just move the gaps a bit out to stop the arc of the OBIT, now any kick back will fire the safety gap. The safety gap is a good monitor as in tuning if it fires all the time you are out of tune big time. It should fire once in a while but no all the time. This is saving your transformer ever time it fires. I find a 2k ohm resistor and a 2000pf door knob cap to ground works well for low pass. Put a signal gen on the low pass filter and watch as you raise the freg. At about 1000hz the signal should go away. This ensures you really are passing HF to ground.

Rgs,
ch

P.S. I can send you a few 2000pf 40kv door knobs if you like?