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If I remember correctly, those black and blue plugs are part of the auto trans harness. They have CAN bus lines that need to be cut and reconnected since there's no more auto trans to close the CAN bus circuit.
When I did my manual swap, I kept the original harness since there's really no difference other than the auto trans connection. All I did was cut the CAN wires from the body side of those connections and reconnect them with butt connectors to close the CAN bus.
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