I have a 2005 flhtci, stock motor with a screaming eagle air cleaner true duels and kirker mufflers, it has been dino tuned. Reasently it has developed a miss at 15 to 20% throttle, or right about the range to hold speed. a little acceleration or decelleration and it goes away, at low speeds if i run in a high gear to keep the rpm below 2100 it is ok. I am thinking it is a throtle position sensor problem.
What tuner do you have? You can test the TPS with a meter to see if it sweeps smoothly or has any blips in it.
Looks to be very powerful software. If you have the dongle, cables &software, I am sure there is a "Data" screen that will allow you to see the output of the TPS as you twist the throttle. Looks very similar to SE Super tuner setup.