Why does my Hayabusa run poorly at half full throttle?

Sounds like you could have clogged injectors, leaving gas to sit in the tank will become gummy, especially race fuel.

The first thing to try is our Wynn's power charge fuel system cleaner.  Drain old fuel out of the tank and use the power charge with 2 gallons of fresh pump gas. We also have the GasTapper in stock, which makes draining fuel from the tank much easier.

You could also have a bad battery. The additional load/heat of the 1397 kit, could cause your bike to run poorly after it heats up if it has a weak cell.