dnz

I have a 36-1 on a bandit motor with the stock pickup and no issues. Where is your missing tooth located? From memory tooth #1 should be around 60-80 degrees BTDC (don't quote me on that, it's in the manual somewhere) for an inline 4 as the crank speed in this position is the most consistent. Like others have said, running without plugs should mask this problem for now. Is your sensor gap similar to the stock set up? What type of trigger wheel do you have? The width of the tooth should be about the same as the sensor pickup to give a precise signal for the ecu.

I have a microsquirt on a B12 with a 36-1 wheel and found the missing tooth needs to be around 90 degrees BTDC to get a constant speed as thats half way between compression cycles.