ECU being bad. Former owner probably couldn’t figure it out so they rigged up a bypass to accommodate.
Best thing might be to run a wire continuity test from the ECU socket to pump controller and do the same for controller to relay (cut wire). Can always run a new line if needed to get things back to normal.
If you have some electronics knowledge - not hard to check ECU connector to verify FPC signal is actually there. That should rule out for sure no ECU issues...