Can you check these items for me.
1/ Is your chain adjusted correctly, to loose causes the bike to surge.
2/ Check the free play in the rear sprocket hub, there should only be a few mm of free play. Grab the sprocket & push it back wards & forwards in the direction of the chain, bike must be in neutral. It there is allot of free play, remove the rear wheel & renew your sprocket dampening rubbers or add bits of inner tube to the rubbers to take up the free play.
Come back to me after you have checked these items.
Some info on ECU's below. What is you last 2 digits of your ECU 00 or 01?
http://www.xt660.com/showthread.php?t=8546