With all due respect, your circuit is not going to work very well. C1 and C2 are effectively in series across the SCR and when it switches on it will short out those two caps with a HUGE current that will damage the SCR as well as wasting lots of energy. Get rid of C2 for a start. Having done that, when the SCR is triggered, C1 voltage will resonate down to zero, at which point the HV pulse transformer primary current will be at a maximum. The transformer inductance will will then keep pushing the cathode end of D1 below ground, causing current to flow in the secondary of T1. This is not good.If you could somehow disconnect D1 from C1 during the discharge period this would be better. Maybe use another SCR instead of a diode. This SCR would easily switch off every half cycle of T1 output voltage. Just make sure you trigger the main SCR in time with the AC supply voltage to T1.
Edit -> I just realised T1 is a HF tranny fed from a mosfet. I was thinking it was a mains transformer. In that case, just shut off the mosfet drive before you trigger the SCR. You will still need to isolate D1 from C1 because of the below ground resonant voltage swing. And use a flyback converter for charging the cap because they are a current source.