Would you classify your backfiring as a lean misfire? That is what I have. I also had an issue with the throttle body but it was due to the airbox being pushed back as explained on the wunderfest tread, not a backfire. I rerouted some stuff under the airbox and its all good now. I do still get an occasional lean misfire, but it doesn't effect the throttle body.
2012 KTM 690 Enduro R
2007 KTM 250 XC