http://www.xt660.com/showthread.php?t=16787
I started this thread some time ago which does wonder off a bit but I think it may cover the problem you think you have - As you may read I fitted a 14th front sprocket as a fix - I'm not suggesting you do that, it made sense to me at the time (and still does) as I was doing a lot of off road work too and it certainly helped in that senario.
I now have Kevs fuel mod, the DNA filter set up and a single exhaust fitted to my Tenere plus a few more miles on the clock since then. The engine will change after a few thousand miles on it anyway but I would certainly say (as others have said above) its a different bike now that the air can get in and the gases out easier.
I would say put a few thousand miles on it then re-assess and consider the mods.