So, youre initial issue was a result of CAN bus errors, caused by water ingress into the TrCM. This had a knock on effect (due to the CAN data corruption) into other control modules. I assume the TCU was changed erroneously because the transmission was going into limp mode when it "lost" its CAN data exchange.
There is, in reality, unlikely to be a fault with the "new" ecu (assuming it is roughly of the correct type. All these modules are now "coded" to your car, and that includes the firmware (the operating instructions) and the calibration (the operating variables) data. These devices are also fully 'adaptive' and aim to learn your driving style and modify their shift points etc to suit you. As such, if this adaptive data has not been properly reset, the TCU may do funny things, or if the coding is incorrect, it may also not operate exactly as before.
If it were my car, i'd want to have the following done:
1) an independent review of the CAN data to ensure the bus is viable (using software that records the raw data stream and identifies arbitration and bit errors)
2) Talk to VW Uk to identify the exact variant coding for your car
3) Get the TCU flashed with this s/w and the adaptive tables cleared
4) Once 'fixed" data log some important parameters to validate the fix is working!