My bad Chris... I'll eat my words on this one, you clearly do know what your talking about, sorry mate. I'm not an engineer, I'm just a sparky with an avid interest. So I'm looking at your graphs, particularly the thrust at the wheels one, there's clearly more thrust with the shorter final drive. I'm not arguing the fact that this will happen, It's obvious with a shorter final drive you generate more torque. What I'm seeing now though is that with the shorter final drive, your clicking third gear at around 42km\h, and second gear is used from roughly 30 - 42km\h. I understand you have taken it from 1 extreme to the other, could you do a comparison where it's not so extreme?
I would love to see another graph that could take in the time taken to make a gear change. It's all good to plot this stuff in a perfect world, but on a race track where you could fall outside the ideal speed for a gear in a certain corner, short shift, or ride the limiter, the deal changes.
On a drag strip, no doubt, if you can change the gears fast enough, shortening the final drive will get you there quicker, but on a race track, I'm not convinced it's a sure thing.