OK, so I talked to the service manager at my dealership about this issue. He said I am not the only one he has heard this from. After talking we concluded that the transmission had learned the way I was driving it in the beginning basically babying it. I followed the manufacturers recommendations on breaking the truck in, not the way I typically drive. He said he would like to try resetting the learn values on the transmission and see what it does and then get feed back from me at next service (5000 miles). So far, and I know it hasn't learned my driving habits yet, but it is much better already. The quick shifting from take off that makes it down shift after 3rd or 4th seems to be better (1st, 2nd, 3rd, 4th, 3rd, 4th, 5th, 6th, 5th, 6th). The stuttering, which was really my main issue, is not as bad either. Still seems to be there, but not as often and not as noticeable. Hoping for more improvements as I get more miles in on it. Will update later.