Jake, it's not the transistor on the timer board at all, but the MJE521 on the ignition board being destroyed by the fact that at less than an idle speed or engine not yet running, the signal to the SCR gate is not turning it off. As it is doing this, it acts like a dead short to the circuit, which in turn makes the MJE521 turn on too hard heating it up while it is trying to pump more and more current into the transformer primary winding. It is a thermal runaway situation, where the transistor gets so hot it can't turn off. I registered over 5 full amps of current draw from the transistor which is past the rating of 4 amps.
This problem only popped up after the last version change. Take a look at the "engine running?" lines to find what is different. I'm sure you'll see the problem in that area.

John