didnt know how to title this any better, but with having the computer tuned for modified cars, some aspects are "turned off" such as misfire codes. What im trying to say is, if the motor was to have an issue that might not be easily detected, will the SES light still come on. My common thought would make me believe that with any major problem in the motor, the affects will be amplified the more modified the engine. A misfire on a heavily cammed motor would prob yield a huge miss feeling as to a stock car correct? just a thought

 

A heavily cammed car might have a miss that would be mistaken for cam lope as well. I've heard of that before. Typically, one has to turn off the misfire detection in the PCM (for OBDII cars) with medium-large cams because the cam can make the PCM think the car's misfiring.

Disabling certain functions in the PCM, like EGR, AIR, rear O2 sensors, and such doesn't prevent the PCM from knowing that it has an issue. As long as you only disable what you have to, you should be fine.