Megasquirt PNP Gen 1 no spark on 1 and 4
 

I was at an autocross this weekend and the car started up and ran fine. Let it warm up in grid and shut it down. When I took my run the car was running like crap. Still 14th fastest out of 65 drivers with on one run with 2 cylinders.

Came back to grid and diagnosed that I had no spark one cylinders 1 and 4. Since I switched to COP a month ago I assumed that was the problem. After checking the wiring and re-soldering some connections I still had no luck. After getting back home I checked the CAS and one of trigger signals wasn't working while cranking (checking with a volt meter). So I got an NB CAS off ebay. The CAS that was in the car was the original optical NA style. Problem is I'm still not getting a trigger signal from the ECU. I've checked the CAS signals at the ECU and they appear good. Check the ignition trigger signals at the ECU and only one is working. I put back on the stock coils and igniter and same thing, no spark on 1 and 4.

I'm thinking it's a problem in the ECU. Might have done something stupid while messing with the ignition wiring in the pits. The NB CAS should work shouldn't it? Is there anything else to check? Thanks.

Wait wait..you got an NB CAS? You mean NA8? NB uses completely different seperate cam / crank sensor. (I'm assuming your car is an NA).
You also can't test the cam/crank sensor signals with a multimeter. You need an oscilloscope. Luckily you can check them using Tunerstudio and the tooth logger.
Also if you're getting spark on cylinders 2 & 3 while cranking then its not an issue with the CAS as its reading rpm correctly or else the ECU wouldn't fire the ignition coils.

Yep, it's an NA8 CAS. The car is a 1990 with a 1.8 swap.