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a coil gun uses powerful magnetic coils to fire projectiles. You need amps for magnetism, not high volts. You need capacitors with higher capacity, lower voltage ratings. And you need lots of them in parallel. 100KV at 1 amp will have the same magnetic force as 12v at 1 amp. Magnetic forces can be measured for a particular coil in amp/turns. This is the amps x the number of turns in the coil. You need as many turns as possible, and as high an amperage as possible.
you can wire a second MOT in series with the first, fully short the secondary on the second MOT, and you should run a lot cooler on any setup you use. I get 45 minutes using mine without risk of meltdown/smoke. Not sure EXACTLY why it works, found it while reading about transformers in material from the early 1900's. I think it is a sort of inductive resistor, which allows for the absorption of extra power on the circuit when your primary is not running, so you have a resistor that reacts to your use of power. That is at least how i think it works, the writer had a few theories of his own.
How Electronic Switches Work For Noobs: Relays and Transistors