Was the water properly drained from under the carpets? There are harness connectors near both driver and front passenger feet that can corrode from water trapped there. Thing is, most if not all transmission wiring doesn’t go through that area.. it is in the engine harness that goes through the firewall directly into the ECU (with built-in TCM) mounted on said firewall. Still, these systems are complex and other wires could definitely contribute.
I agree with
@linuxgod find a competent mechanic to go through the above procedures. It’s just too coincidental for the inside of the truck getting wet IMO, and getting all that water out should have been a priority. Btw it is very easy to pull the door sill trim and look for water. Just pull up. If water remains it’ll be toward the front with your wiring harnesses lying in it.