When they figure yours out, let us know, because mine is doing the same thing. I also have the manual and notice the hesitation as well. Sometimes worse than other times.
Just got my truck back, not fixed but they know what the problem is. It seems that with whatever the latest flash is, the trucks will go into regen at any speed to prevent city drivers from plugging the dpf. The problem with that is, when the truck is trying to regen, there is a delay programmed into the throttle which is much more noticeable with a manual trans. That is what my trucks problem is, and I was told that Chrysler is aware of the problem, and they are working on a new flash to correct it.
So, now I feel like a Ford guy back in 03, eagerly waiting for the new flash so I can see if it will make my truck like it's supposed to be.