So I have a 98 civic ex and I recently swapped from a y8 to a y5. The swap went fine. No check engine light and motor ran fine. I took off the intake for a day and it drove fine, however with a check engine light. Is that because of the intake? / And I just put new headers on it today. And I noticed when I go to turn it on it has a hard time starting and then on top of that the idle fluctuates. The car will drive, but it will fluctuate when I attempt to ay the radio or turn on headlights. Someone help.

 

Are you using any HX parts then? The HX ECU intake etc for the Y5 is ENTIRELY different from the EX. It may work to fairly well keep the car EX except for the block and head.