Hi Simon, have you also raised the idleing speed or tickover at closed throttle to at least 1450-1550 rpm?

You will find that this simple fix might work wonders as often the tickover on these bikes is too low, and when you let go of the throttle the bike starve and causes it to surge. In some cases we've had to adjust also the TPS, throttle position sensor to the correct angle.

I would recommend that you join the XT Supporters http://www.xt660.com/showthread.php?t=1475

and Ask Kev in a provate message to give you a step by step guide on how to overcome all these little issue, I guarantee that he will be able to help you minimize the problem altogether.