1. What was reported in the original post, sounds as if there has been some adjustments from standard. Namely carb settings. I would put these back to standard (all standard carb setting in KTM manual, with specs). Standard setting before trying moving away from those and then only one setting made to try. You will always have a known situation to go back to.
2. Try raising the tickover speed, 1400 to 1500 rpm is about right.
3. Mine used to stall/cut out sometimes for no apparent reason if the air filter is dirty/blocked, clean out airbox properly with blue roll/tissue and maintence spray and fit a new/oiled filter.
4. If you think its electrical - The underseat fuse box towards the back of the bike above the battery. The fuses have a habit of loosening off and being slightly baggy in the holders. You can push up tighter the fuse holder grips for the blades with a very small screwdriver or scriber. This makes them grip the fuses tighter. Could be that cutting out the ignition circuit with vibration, but you did'nt mention electrics cutting out at all in the original post.