So turns out that last start was just "lucky", as Brian at PE put it. Apparently the PE3 can't deal with a 12-1 trigger wheel and the stock 3 tooth cam trigger, so we swapped the trigger wheel back to the stock wheel (12-0) yesterday. A little bit tricky, since the clutch cover wouldn't actually come out of the frame, but it was a relatively smooth process all things considered.
After swapping in the stock wheel, we changed the ECU settings to reflect the proper trigger wheel, and it fired up right away. Timing looked good, and the engine ran, idled, and revved just fine.
A little more work needs to be done on the intake to strengthen it; it was flexing a lot more than we were comfortable with.