I don't have the Pro Taper bars, but I do have bars that are even higher. I ran my throttle cable up and over the back bone of the bike directly underneath the tank. My dad's bike does have the Pro Taper bars and I ran his throttle cable through the little "window" next to the coil. This gave me enough length.
What year is your bike? If its 2000 or older I'd be happy to send you some pictures of what I did. Let me know.