Where is your co set to & what are your last 2 digits on your ECU?
http://www.xt660.com/showthread.php?t=8546
You can safely turn the dial all the way to the 10 O'Clock position. With your mods the dial could be set between 1 to 8 O'Clock. Start at 1 & riding the bike turn the mod clockwise until you find the smoothest ride & leave it there.
Also make sure your chain is adjusted correctly & that there is no free play in the rear sprocket holder as these 2 item also cause the bike to surge.