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The transmissions are different. The M12 (Z06) starts with a lower (2.97) first gear and the spread is different thru out. Go to the Corvette Museum website for a complete breakdown. There is also some differences in the sycros.
I had read somewhere that the driveshaft and rear were also different (read: stronger). Recently my car was apart at the dealer. The rear was sitting on the floor and I could see that the ring gear has cuts in it that are not in the standard rear, even though the gear ratio's are the same (3.42).