Just guessing here. If the transmission was submerged I would think that there could be several possibilities. Since the OD light is flashing, I would suspect an electrical problem. I would clean the electrical connections first, especially any grounds.
If I understand correctly, a transmission error code is read off of the OD (over drive) light flashing, not the CEL light. On the OBD1 system you would bridge terminals E1 & TE1 of one of the diagnostic ports. Turn the key on without starting the car and read the OD light flashes (same principal as the CEL flashes). I believe the common ones are 42, 61, 62, 63, and 64. If you have OBDII I believe that there is a different reader that is used for the transmission and a third for the air bag system.
Random thoughts: 1)The torque converter OD lockup is electrically controlled. Could it be permanently locked? 2) If water got into the transmission fluid, it is conceivable that the fluid got gummy and gummed up some valves or solenoids. I’m not certain what to suggest but there may be a cleaning additive that you could circulate through the transmission to disperse any water and dissolve any gum that may have jammed up anything. 3) Neutral start switch may have an electrical problem.