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California Diesel's have different emissions devices then the rest of the free world. The EGR valve is one of them, I am not sure what it would affect but I doubt it would mess up the tranny.

You should know by now that California has to be different from the rest of the States, the California Diesels come with an EGR valve and a few other minor things and a Catalytic Converter, where the rest of the states only have a Catalytic Converter, which in my opinion is a waste all it does is help to roast my turbo and cost me fuel milage. I don't think your problem is a computer related issue for the most part the engine and tranny are not computer controled, I would look for a sticking valve in the tranny valve body, take it to a GOOD tranny shop and they should be able to troubleshoot it, the dealer will only hook it up to a computer and read the screen for you.

Good Luck