BMW E65 735i - 2003 (N62 32 valve - V8 engine)

Doing swaps in a BMW is difficult with the myriad of electronically controlled systems. Kudos to you for getting things to work as well as you have, that is no simple or easy task.
The DME and transmission control unit are not, "Married" to the ECU as they are seperate control untis and for the most part can be called, "Stand-Alone". However, take that with a grain of salt becasue they will be looking for certain voltage signals in the amount of voltage sent and the pulse length in some cases. Since the engine was close enough that the DME would switch over, there could actually be some variance between ECUs and the DME could still work, because the voltage signals were the same from the same pins. This is something that all car companies will tend to follow as a cost effective practice as having more than necassary ECUs to cater to engine configurations that are near the same would cost money in manufacturing, repair and replacement parts. So, you did get lucky in some sense as there is one huge problem that you will have trouble overcoming unless you get lucky or shell out hundredds of dollars for a factory BMW service manual. They will have the ECU PIN OUT chart that should also come with test specs for checking the ECU. This way you could check the ECU to see if the pins would be putting out the correct signal and from the right location. BMW will not release these otherwise and I am not even sure if the service manual will go as deep as you need, even though it must so ECUs can be tested. Then you run into another issue, do you need to see another pIN OUT to compare ECUs Do You need the PIN OUT for the connector for the DME or transmission control unit? You may need to knwo what the connectors are and there position for the DME harness as you may be able to move a terminal to another position in the connector for it to work.
As far as the transmission control, it is seperate as the DME is but there is something that makes this even harder to deal with than the DME. Automatic Electronically controlled transmissions are incredibly picky and difficult to work on and diagnose. Even BMW will generally just replace the tranny if it seems to be at fault in a warranty situation as diagnosis costs more than replacing the unit. So, you may get lucky as the configuration is pretty much the same, but will other parameters, from the DME or other sources, keep the tranny control working correctly?
It is nearly impossible to say. If you have a transmission specialist that really knows there stuff, I woukld tend to go with that information as it takes years and years to learn how BMW does things and then it takes access to information and then it takes the talent to implement the work at hand. BMWs are a different beast and automatic transmissions even from a 1977 Oldsmobile are difficult to work on without the electronic control. You have to consider that the DME is isolated in the fact that most of its inputs are from other sensors in the DME system. The transmission control takes input from Engine, Load and DME circuits and sensors as well as signals from its own system. It is worth trying as trying to get it to work is about the only way to see if it will. You might callsome high performance BMW shops, I don't think you can get in touch with the BMW personel who make 500 series into M5s, and that might be a good source. I would not take information you find in enthusiast forum to heavily unless you can find someone who has done the same thing and they have a good and long reputation on the forum.
You are kind of taking a fairly well educated shot in the dark, but that is the new age of hot rodding, dealing with the on board computers. Thank goodness they aren't Windows based.
Good luck and I hope it works out well.

I would use the one from the donor car. It has memorized the inputs from that transmission.