I'm pretty sure that Motowheels uses the ProTune Powermap to remap the ecu. There are tunes (maps) available for nearly any mods that you make. Just tell them what your setup is and they can load the proper map for it.
2010 696 ProTune Powermap programmer, EvoTech tail, Quat D Alum slip ons, Artrax wavy rotors, K&N, 14T, bar risers, G2 Throttle Tamer. Still working on swapping all of the black plastic over to carbon fiber. Oh, and no more ugly charcoal canister!