I re-read through most of this thread and saw back where you were describing an odd shift between 3 & 4. I'm getting this as well about 50-60% of the time, especially when in normal mode and driving around town. I figure I would give the truck time to "learn" a little more, and if it didn't go away I would pull the negative for 15 minutes and start the thought process over again.
I was also getting a little odd shifting between 8th and 9th, but that seems to have worked itself out. The 3/4 shift seems to be getting a little better as time goes on too. It almost seems like 4th gear is a little too short of a window, so it shifts in and wants to shift out right away but ends up having a lag between the two. I notice it more on upshifting more than downshifting, but it does happen both ways. Sometimes when it feels smooth, it almost seems like it just completely skipped 4th and went straight to 5th.
Glad you are finally getting it worked out, I'll be keeping an eye on your updates. Is the 3/4 shifting the main reason you wanted to go back to stock, or was there something else I missed?
---------- Post added at 09:47 PM ---------- Previous post was at 09:28 PM ----------
Took a road trip this weekend, 356 miles each way. On the way down, we got in a row of faster moving cars, and I was in the middle of the group. I went to pass a slower vehicle, and at around 80-85mph with increasing speed and RPM, I heard what sounded like a gunshot in front of the firewall and the truck stuttered and had a hard time gaining and maintaining speed. I was able to complete the pass (had to with another car coming in hot behind me), but I let everybody pass and turned off at the next opportunity. No codes thrown, and no boost being made. My initial thought was that I blew the turbo's, but it ended up being the hoses on both ends of the intercooler. It appears as if the dealership may not have tightened them well enough when they did the install.
The dealership that I took the truck to the next day did the fix as a courtesy for me. I was pretty shocked, and slipped the mechanic a nice tip for some lunch money. They said they weren't overly impressed with the clamps that are provided by Whipple. My hopes are that they are sufficient, just may not have been tightened well enough initially.
I am getting an odd shift at 3/4/5, but it seems to be getting a little better. It feels like 4th gear is too small of a window and it already starts to shift out of it as it is shifting into it.
Here is my details for the trip back home. We went through a pretty heavy sleet storm for the first 1/2 of the trip, so we were moving along around 55-60 at times. I was able to kick it up some towards the end of the trip as the roads dried out. There was a fatality on the road Friday night due to somebody sliding across the road into an oncoming Jeep, and we saw a pretty bad wreck coming home today too. The math equated to about a 65mph average for 5&1/2 hours. I'll take this gas mileage any day.