I've been told both ways about emissions tests in Cali - that you both can and can't change gearing.
From what I've been told, you can, as long as it's something that comes with your vehicle during the same production run. I've been told that if the engine speed doesn't match the dyno speed for your VIN, you fail.
It's been both ways verbally. Without being there, or looking up the laws (which don't apply to me, so you know how far that's going to go...
) I can't say one way or the other for sure.
I do know that there is very little that is legal according to the EPA when it comes to engine swapping. I posted a PDF of the abstract somewhere, either here or on CustomTacos.com.