Yes, but if the power remains the same but moves (say) from 7000 to 6000 rpm, surely you'd need to change the gearing or the bike would be undergeared? Assuming the gearing was right to start with, which it seems to be.
Edit: 108mph would become 92mph. It'd feel good getting there though. 
Once you raise the gearing the torque at the rear wheel goes down and it ends up slower.
I wrote my programme based on the original programme in John Robinson's book, which now appears to sell for a stupid price.
http://www.amazon.co.uk/Motorcycle-Tuning-Four-Stroke-Robinson/dp/0600333655
I added better graphing and torque through the gears. One day I will sit down and rewrite that programme.
You're right...... If you took a standard xbr, or any bike, and raised the gearing you'd lower the rear wheel torque. But........
We're talking here about a different bike than the standard xbr. One where the engine power and torque will have been shifted 1000 rpm down the Rev range. So, if you want to keep the rear wheel rpm matched to peak power engine rpm you'll need a different overall ratio. True, if you want to raise the rear wheel torque, then lower the gearing. But to attempt to keep the maximum power allied to the same road speed on an engine which makes that max power much lower you'll need a different overall ratio. Higher gearing.
Do the maths. Assuming the same max power (which the two examples pretty much are) and assuming the same road speed (which we can, because we already know that the power we have will get us there), then we're saying that the final rpm, the rear wheel rpm, will stay the same. Using the power formula and cross multiplying you will compute the same rear wheel torque. You have to! The only two variables are both the same value.
So, to achieve the same rear wheel rpm but with an engine which is giving that same power at a different rpm we will need a different ratio.
Would you not agree?
Edit: if we had full power and torque curves then even better. We can plot rear wheel torque curves for each gear and compare to stock xbr. We can also see how the power tails off after peak power rpm. Maybe that would influence our overall ratio choice. But the stock xbr is a known quantity and so is valuable as a datum point.