Have you thought of turning up the boost a little but to make up for the higher altitude? Plus if the altitude is the problem they would lean the fuel out and normally they drop the boost pressure a little. However if your plan is to build the car then you "prep" the motor for a bigger turbo.
I just picked up my '10 Celestial Blue Speed last weekend. had a whole 57 miles on it now it has a monstrous 306....
Not that many Celestial Blue speeds....was it not a common color for the speed3?
it sounds like a turbo or fuel issue...possible a combination of the 2. Do you know if the turbo itself is the same and if the turbo is still pushing the same amount of boost?