If your car was an auto and now it is a manual the check engine light will be on for the lack of connect to the auto shift solenoid. You need to clear all codes then work from there to find the idle issues. CEL can cause more issues that more people think. I have an auto P28 ECU on my manual civic and it runs, but not well.
Adjust valves and check the spark plugs and compression. Not sure what you are running in what, but if you have low compression the engine might idle. When you reinstalled your rings and pistons did you check ring gap clearances and install the gaps offset? If you have low compression, that might be a consideration?