Here is your approximate repair flowchart:
Drop the pan
After the bulkhead connector position checked ( check the bulkhead connector seated all the way inside ,open and close the locking tab once again)
Check the main TCM connector pins resistance ,on the main engine harness all the way to the PCM,after checked ,what DTC do you have on your HS-CAN compatible diagnostic tool?
If the harness is ok and the bulkhead is ok and still communication issues are present ,replace the TCM ,the valve body to transmission seals (four cylinder one and the rectangular one) and perform TCM to PCM pairing process if the TCM changed to used one.