Yep...just went through this with my 07 Dyna. Take the fuse cover off, start the bike ,and gently wiggle the system relay and EFI control relay. If its like my Dyna, the bike will miss/and or die. This is a common enough problem that I carry those two relays in the tool kit.

 

Mine did that same thing, turned out to be a wire harness to rear injector, no code, later found out to be a recall memo sent to dealers only.

 

Sorry didnt read the whole thread but you should check your main relay.
Beside the fuse panel.
Mine did exactly what your saying then stopped altogether.

No codes were thrown but it shuts down the fuel and ignition system. Started right up afterwards but then all of the sudden nothing.

$5 part and I wasted a day on the trailer because of it.

Good Luck.

 

Had this happen to me on a 1200 mile trip. Engine would cut out for short time then take off again, did this 4 times in the last 600 miles. With the help of forum members I narrowed it down to the system relay fuse 8 dollar part and running like new again

 

Had these same symptoms on my 06RG several weeks ago while riding back from central PA to VA. Just a couiple times but enough to catch my attention. Checked the wiring and air filter. Changed the fuel filter, checked the plugs, nothing really stood out as a problem. Rode it some more and it stuttered a few times. Took it to my mechanic. He rode it for a couple days but didn't experience the problem. I took it back and within a few days it stuttered again. Went through all the connectors on the throttle body and added injector cleaner and the bike ran fine for a couple days. Headed out last week on a ride from N. Virginia to N. Kentucky and the stuttering came up again but it got really bad to the point that the bike was only running on one jug and it sounded like it lost its tuning. I hauled the bike home in a U-haul truck and took it back to the indy. He rode it and experienced the problem so now he has something to work with. He changed out the crank position sensor but the bike still ran rough. Next item was the head temp sensor but I didn't want to hang around to see what he found. The bike has been there since Saturday but he hasn't called with a progress report, but then, I didn't really want a report except that he found the problem and fixed it.

 

let us know the outcome Im curious...Thanks