When the check engine light comes on after it shifts once or twice and stays on until i turn the car off. It only started doing this once i swapped in my b16, also my s3 button flashes the hole time also, all help would be appreciated.
Thanks, Andy
What year is your car? What year is the ECU from? I am assuming that you also did an auto to 5 spd conversion?
I might be able to help you out… you check engine light could be a couple things. First, b/c the s3 light is flashing. That happened to me when I first bought my car… after a few months of trying to firgure that **** out it was a littlt solenoid on the side of your tranny, kind of parallel of your tranny dipstick. I can’t remember it for the life of me… I want to say your shift solenoid? But after I got mine replace it went away. That could cause the check engine light… also for the check engine light, check your O2 sensor… replace mine and no more light! 
I hope this helps you out… If you have any questions ill try to help ya out!
Good luck bro!
^
I assume you still have the auto trans. on the B16A. Make sure you’re using the correct JDM B16A ECU designed for an auto. Once you’ve got that figured out then you need to see what code the CEL is throwing. That will help you figure out your engine problem. Because the S3 light is blinking that means you also have a trans. code. There’s a little box under the dash just above the brake pedal that will tell you what code the trans. is throwing.