I didn't want to write all this up, but unfortunately some people wont except a simple "it has to be USB" 
It has to be USB, because the connection will be via the back channel of a wireless video system that has a USB "back channel". And that system has no wires hanging out to connect pins. USB will also be much more future proof, if I have to use another setup. This is not ment to be a toy setup on a table, its for a professional film production wireless follow focus system. The video system transmits live view of the camera to a remote monitor. The input for the Arduino will be a puls encoder operated by the camera assistant at the remote monitor. The data beeing the number of steps to the next focus point. The second Arduino will use that data and drive a stepper motor rotating the fokus ring on the lens. Once programmed the system has to work independently of a PC. And to keep it simple on set, I won't use an extra wireless system for the focus control - the video transmitter is enough (it has a USB 2.0 channel built into it).
You'll need to write a driver for the Arduino to use to command the host shield. Not a trivial task.
I thought there is a library for use with the USB shield? Where can I find information about writing a driver?