2010 runs like crap when warm. dealer says????

I have a 2010 550 sportsman EFI and electric steering. It was riding great, stopped put it in Neutral, idled fine. put it in gear and it started to load up and backfire, got it back in Neutral and it cleared up. put it in gear and it backfired and bucked.
so it runs great in park and runs like dirt in gear. even if it is in gear and Idling it runs like dirt.
This problem only happens when it has warmed up. When it is cold runs great in gear and quick test drive.
It is at the dealers for about one month, nothing on their computer. They have changed out the crank sensor, tested the fuel pump, checked the fuel injector system, tried another ignition module and check the wire harness.
SHIIIIIIIP WHAT THE HELL.
So I am thinking could it be the gear switch on the tranny? Does this switch tell the computer to do something to the timing or injectors? Why am I saying this because in the beginning it ran fine in park or Neutral, Put it in gear, no load no throttle and it went right into running like crap, got it back in park and it cleared up.
I am kinda desperate for help.
thank all.