How long did you leave it running after it started previously? Why did you replaced the SKIM and lock cylinders? Was the car previously stolen or gutted?
I'd suspect the the keys with their built-in transponder chip, the SKIM (module) and/or the computer don't all match. If you had no other reason to swap the SKIM and ignition keys you should only install the Stage 2 computer and program your vehicle's VIN to the computer.
If one or more of the components do not have the same "secret key" encryption code, you'd need to have the dealer try to program everything and I suspect most won't want to touch a car with all different computer and SKIM that have used parts swapped in. Best bet would be to reinstall your stock SKIM, lock cylinder so the stock keys can be used, then have your VIN programmed into the new S2 computer.