Josh - Your inbox is full so I'm replying here instead:
Trying to think high level here. I'm a software engineer and know most of my colleagues think too deep before looking at the big picture.
Since I'm not a NAG1/5gtronic expert I'd say we need to clearly understand how the TCU determines its speed readings. Is it from the two sensors in the valve body/conductor plate or is it from the sensor in the rear diff? I know my 4r70w in my Ford builds its shift logic on the Output speed sensor (magnetic sensor) in the Trans body (all other sensors are irrelivant since its in a 57 Ford but drives great without any codes

)
So what reads the gear ratio in the 5gtronic? If the TCU cannot read what it expects, will it toss a code and slip or should it clunk into limp home?
Here is what your Trans provides ML500 722.666:
First Gear Ratio

1)
3.59 * *3.59 min 3.59 max
Second Gear Ratio

1)
2.19 * *2.19 min 2.19 max
Third Gear Ratio

1)
1.41 * *1.41 min 1.41 max
Fourth Gear Ratio

1)
1.00 * *1.0 min 1.0 max
Fifth Gear Ratio

1)
0.83 * *0.83 min 0.83 max
Reverse Ratio

1)
3.16 * *3.16 min 3.16 max
Here is what the ML320 TCU wants to see:
99 ML320 722.662:
First Gear Ratio

1) 3.93 3.93 min 3.93 max
Second Gear Ratio

1) 2.41 2.41 min 2.41 max
Third Gear Ratio

1) 1.49 1.49 min 1.49 max
Fourth Gear Ratio

1) 1.00 1.0 min 1.0 max
Fifth Gear Ratio

1) 0.83 0.83 min 0.83 max
Reverse Ratio

1) 3.10 3.1 min 3.1 max
What I'm still trying to figure out is IF the TCU is hard coded to the gear ratio or if it can be adjusted? ML320/430 trans in an ML500 (example). And IF this is hard coded, must you utilize the ML500 TCU if you use the ML500 Trans?
TBD right?