trism18 -
Yes, there's an effect on performance. Taller gearing to reduce highway RPM will reduce acceleration. The opposite is possible too, you can have snappier acceleration if you set it up so the highway RPMs are higher. If you go too tall the clutch tends to wear quiclky because you have to slip it a lot to get moving with the higher final ratio in 1st gear.
Messing with the transmission ratios is also possible and you could have normal ratios for 1-4 and a higher overdrive 5th gear for cruising, but because the gears are in the engine case and special ratio gears would have to be custom made that's a rare modification.
The old CB900 Custom has a high/low primary gear selector, low for tearing around town and high for freeway cruising.