I switched from an M6 to a 4L80e in my '06. Actually, I switched to the 4L65e first, about three of them, then the 4L80e.
It's not that difficult if you get the A4 harness and TCM.
In short, controller-wise, swap out the engine harness, add the TCM, reprogram the ECM and TCM with the A4 OS using HP Tuners. Use a Tech-II to reprogram the PIM and IP to A4.
Done!
You'll retain cruise control, speedometer, torque management (if you want it), etc. And you'll be able to tune (and log!) both your engine and trans with HPT.
Aftermarket controllers are costly, do not retain features like cruise control, and are likely
more difficult to install than an OEM harness.
You can build an adapter to run the 4L80e from the 4L65e control program for less than $20 in Radio Shack parts (two relays, two resistors) and a couple hours of your time. And the only transmission DTC you'll need to disable is P1870, which HPT
does give you access to.