OK, caveat: I have no experience with wood burning with electricity [you're creating Lichtenberg Figures, correct?]
But, just based on Electronics: if the Microwave Transformer is getting hot, and popping the circuit breaker, then that means the resistive path is allowing too much current to flow. There are two things that can cause too much current:
- Resistance is too low
- Voltage is too high
So, either use less baking soda [or whatever it is that you are using to make the water more conductive], OR a lower voltage [which, clearly, is what you're trying to do]
BUT, maybe by adjusting the conductivity of the water, by using less "ionizing agent", you can get some success with the microwave transformer -- i.e. get away with using more voltage.