Is the hub a direct drive? if so, pull the pulses off the hall sensors, the same way the Cycle Analyst does it. There's even a pad on the board for it if your controller doesn't have a CA hookup or the blue speedo wire already.
Any cheap bike computer sensor will do it, or you can get a hall sensor one like this:
http://www.bmsbattery.com/controller/661-s-led770-e-bike-led-meter.html