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Hello my name is ***** ***** thank you for your question.
The TCM is part of the Valve body. When you get cross contamination, the TCM is one of the first things that start to go. The Tcm for your issue is most likely damaged due to the cross contamination. You would need to replace the valve body if there is no communication with the TCM. The U1000 and U1001 is a indication of Control unit failure or communication. CAN system check would verify if the TCM is the issue.
If you changed the Transmission, why did you use the same valve body? You only run risks of damaging the transmission??
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