Need ideas, I'm lost

Ok I have a 2000 tacoma 4x4 5 speed. It has the 2.7 in it. I swapped engines and after swapping engines and tracking down the right valve cover it cranks but it's not firing. Could it be where my truck had federal code engine in it and I replaced it with the California code engine? Can I flash computer or is it deeper than that?
 
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