Hi Bob,
I've had issues with my central locking pump / security system module (CLP/SSM) from a plugged drain and it sitting in water for many weeks. My symptoms were quick battery drain, stalling, and intermittent FOB operation. This may not apply to your situation, but this was my experience. I cleaned my CLP, but noticed that some of the pins in the connector had rotted out. Fortunately, there were unused pins in the board connector, so I swapped them with the rotted ones, and my pump has been working for 5 years now. I have two roadster crossfires, an automatic and a manual, so the water in the truck happened to the other one as well. The second CLP electronics survived the water okay, but the motor that drives the pump failed, so I replaced the motor. That didn't turn out as well, so that's my spare. Anyways, there are many ways the CLP can fail, but when you mentioned you repaired the connectors it bought back memories that the pins corroded away - yours may physically still be there, but they may not be electrically connected. Just a guess.
Good Luck
-Jerry