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As long as you are using a compatible engine/ecm the factory 6l80 will work fine in a swap.
You just have to disable the passlock stuff and make sure you have the correct 60 ohm resistance on the CAN bus so the controllers can talk.
The problem with making stand alone controllers for the 6l80 is that tcm is internal to the transmission and directly actuates the valve body. It's not just a matter of wiring up a tcm to some sensors/solenoids and telling it what to do.