confused computer

[indy240]

I finished building my motor and it's in the car. It ran perfect for my 30 min. break in run, and ran perfect for the mile or two drive i took it on. I fired it up two days later and it seemed like it was missing out a little, not sure why. I'm wondering if the computer will take a little while to learn what i did to my motor and adjust to it. The only thing that should affect a sensor is the cold air intake and the headers. Oh, by the way it's a ka24e. If anyone has any thoughts that may help me it would be appreciated. Thanks