Had the same problem. Turned out the grommet by the A/C drain was cracked and worn allowing water into the firewall then into the floor board. Check the grommet and it will probably be worn allowing water in.

 

+1, Even if the seal/grommet is ok. With three feet of water it could be just going in the drain tube itself and out the lower vent.

 

If your going to put vinyl anyways....then pull your carpet out and look for "the" hole. I pulled mine 3 weeks before I installed my vinyl . There were 3 small holes in the floor, I welded patches in then seam sealed them and then used bedliner on the entire inside. When I installed my vinyl i didn't want to use the insulation underneath because it acts like a sponge and rots the floor , so the bedliner quieted the cab noise down a little. good luck !