Hi, I’m Chris. Welcome and thanks for asking your question!
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Why was this repair done in the first place?
Did you use a junkyard harness?
Have you went back through and double checked every connection, especially the transmission harness connection?
Have you OHM tested each wire from the PCM to the components on the transmission to see if the wires are broken or making poor connection, do you need the wire diagram to do so?
Use the below wire diagrams to ohm test from the PCM connector back to the transmission components Charlie.
As long as it is showing a Ford code like p0171 or U0506 for example.
When you ohm test wires from both ends you should see continuity and no resistance meaning the wire has no breaks in it.