On my 100,000 mile ultra with a Vance and Hines controller, SE throttle body some days when it's real warm it will cut out up to 3500 rpms like someone's flipping the kill switch on and off. Someone's pops and misses. Over 3500 rpms it's fine. No codes. TPS is bang on. Leave it sit for a while and it will be fine. Seems to be when I'm sitting in the heat at road construction when it starts acting up. Any ideas???

 

Make sure the battery is in good order and properly charged. Check for any goo dripping out of the nose cone. That would be your cam position sensor taking a dump. Also check the Crank Position Sensor connector located behind the right side cover. It is the barrel shaped connector by the ecm. Then take the tuner out of line and run the bike to see if it still does it.