You need a laptop connected to the PC3 with the PC3 on the bike and the ignition key turned on.
Use the Set Throttle in order to synchronize the PC3 to the outputs from the Honda fuel injection system throttle positioner.
There is an excellent PowerCommander site download tutorial "Set Throttle" that shows how to do it.
Don't be spooked by the numbers in the boxes.What's more important is the throttle position display that is on the right hand side of the display panel.
You want to see 0 at closed throttle and 100 at open throttle.
Reset and do both Closed and Open, and not just Open as PowerCommander suggests - unless your is already showing 100 at Open.
If you can't get the tutorial for some reason and want it, send me a PM with an e mail address that will accept attachments and I will e mail it to you.