Sounds exactly like a fuel pickup issue, and,, if your inlet sock is plugged you will overheat the pump which makes it worse.. This is based on my EFI experience, not KTM experience..
Once the engine goes lean its going to heat up worse,, and then the problem spirals downward.. As the lean engine symptoms distract from the real problem.
If the dealer cant help you,, see if you can track down a decent sports car or bike race tuner (Track/Road racing not ricer drag action) They can hook up to the engine with their gear and see whats working and whats not.. a couple hundred spent on someone who knows there stuff is cheap compared to a gorilla throwing parts at it..
Bad injector will cause hot pipes as well, but normally that should throw a code..
My drinking club has a motorcycle problem....