Well, first, on track performance is full of pitfalls when it comes to monitering performance, and....as you said, you're running an ITA car. Why should they give any weight to your results> You SHOULD be off the pace, right?
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The didference in the allowable things that you can do to the EP Neon aren't going to make up for the difference in lap times. Besides, who says that the car I will run in EP is an ITA car

Maybe I put the cam in and up the compression ratio with a milled head?

The possiblities are endless (Mad scientist laugh)