I have a 1994 Mazda MX5 with the engine out of a 2004 NB MX5 (BPZ3 with VVT). I am using a Link G4+ MX5 ecu and can only get the car running on two cylinders. I am using the sensors that match the motor, my old motor used a CAS but on the new motor I have wired up a Crank angle sensor and a seperate cam sensor. I am also using a 36 -2 trigger wheel with the crank sensor. I've checked the mechanical timing over the motor 3 times and it's correct, but my trigger offset is 210 degrees. I can start the car with ease, but it will only run on 2 cylinders (1 and 3). If I take -360 out of the trigger offset and set it to -150 the car starts with ease, but runs on the other two cylinders (2 and 4). The ignition system is wasted spark, I was using the original coils from my car but have since upgraded to 4 x ls2 truck coils (still running wasted spark).
Also I have ran the ignition and injection tests and everything appears to be fine in that regard.