On your diagram, number 33 is the gear that meshes with the middle gear shaft. It is different than the gear on your original bike. It has a different number of teeth (which is the output ratio change from Gen-I to Gen-II.) The gear on the other shaft that it meshes with has the same number of teeth between gens, but I would bet that it's slightly different in diameter and/or tooth profile, and even though it's 35 teeth on both gens, it's a different part number between gens.
What I'm getting at is: use the gear from your original transmission in that position. It and the bearing next to it both slide right off of the shaft so it should be an easy substitution.
The other differences between the gens are due to changes in the dog design that was mentioned earlier. The forks, the drum, everything that touches something from the old bike is the same as it was on yours, except that output gear. If you try to use the one that came with the 2008 transmission, I would expect Bad Things to happen. Put your original part on that shaft.