2007 E70 4.8i - Odd Transmission Issues

[Entropy]

My E70 4.8i has 81k miles on it, and since I have owned it, the transmission has been acting odd. I am hoping someone that has experienced these issues can point me in the right direction.

Issues before transmission reprogram:
- Especially when cold, the transmission will shift into 2nd fine, and hesitate during it's acceleration period before it shifts to 3rd (e.g. the car is still accelerating, but the RPMs hesitate/stand still) and then it will finally shift into 3rd. Sometimes it will shift into 3rd before this hesitation event, and then once in 3rd, the RPMs will surge hi-low-hi-low, and then shifting from there-on-out is fine.
- When slowing down, and then getting back on throttle in 2nd or 3rd gear, the RPMs will surge up, then down, then up, then finally back down. It's like it's slipping then catching.

After taking it in for a reprogram, all of the above issues are still present, but now it does this:
- When letting off while cruising, the RPMs dip 200 or so, then resume back where they were while cruising.
- If I am off throttle while coasting on the freeway, and quickly get on throttle, the RPMs will surge up past where they were, then quickly settle down to normal.
- I can really feel the 2-1 downshift when coming to a stop. It's feels like someone pushed the brake pedal hard for a split-second, then let off to normal pressure while coming to a stop. It sort of makes your head lunge forward and then back, and then the car finally stops.

I have done a full transmission flush (2 pan drops; ~11 liters of fluid) and a new filter/pan. Oil used was Pentosin ATF1. I didn't notice any change in performance after changing the fluid.

Any advice is welcome. I am really hoping it's not something mechanical. I am a DIYer, but these transmissions are quite complex.

Thanks,
Chase