The XTX & XTR fuelling is very poor for a new bike, you think they would have got it right by now after 5 ECU updates.
A Power Commander is the best option, as long as you get a custom made fuel map.
As you can see from todays post I have have managed to get rid of most of the surge. I built this fuel map with the bike completely standard.
http://www.xt660.com/showthread.php?t=8546