Find out what "P" codes the ECU is showing and what sensors/systems the shop is saying are not ready. This will help me narrow down what your problems can be.

Another question for you, do you have an aftermarket ECU or a DSM link? Either of these may be programmed not to run certain diagnostic checks at startup or during key cycles (IE EGR if you have deleted the EGR system). If you have a DSM link keep it and buy a stock ECU for inspection purposes. Swap it in about a week prior to your inspection so it has a chance to do enough key cycles to clear the battery unhooked code.

-Kevin