I am with Runhard on this one. Put your factory exhaust can back on. I have a 04 1m efi and I put a can on it before I got it home from the dealer. Long story short it ran great in the mountians but at home it would run good for a second or two then act like I fouled a plug. I never could get it fixed, dealer did all the stuff you are doing servo motor ect.. I came to just live with it and ride it only in the mountians since it ran ok up high. Last year I put on a Jaws front dump and bingo problem solved. Runs great at home and in high elevations. Just for fun one day last winter I tried all three cans, stock, jaws, and the problem can ..... Guess what Stock & Jaws cans it ran perfect, the other can it ran like crap again.
Hope this fixes yours, let us know