I have a 2007 street glide with a 96 to 103 SE kit. 58 km throttle body and Rinehart 2 into 1 and Dynojet power commander 5. Upgrade performed at Dealership 4 years ago. No issue for first two years. Bike starts fine 95 percent of time. Occasionally engine will start to turn over and then sounds like it spits back like on carb system then dies. Subsequent attempts to start fail with engine turning over fine but no fuel or spark catching. Hour later same result. Next Day bike starts fine. No Harley Diagnosed generated. I have replaced cam position sensor. Checked wording for loose or corroded connections.
Check for codes first..
It sounds as though the the timing is too far advanced, too lean on the cold start program,, maybe add some fuel to the cold start enrichener function..
If you uspect the power. Commander, unplug it, and plug the lead into the oem harness, and repeat.. the startup..
Have you done a compression test?, if not you should..
The dealers techs, are limited in what they can do to the bikes tune,, it most be within EPA specs even if you had a monster motor built, the dealer could only tune it as an emissions tune,,, or, to the point,, its foo bad you spent all that money,, I cannot enrichen it past EPA specs,,, sorry your motor may melt,, complain to the epa..