If im not mistaken, if the air conditioner drain is clogged this will cause overflow into the floorboard. Im not 100% sure on newer vehicles but on older ones rain will enter into the air inlet (on the passenger side between windshield and hood) and will drain out the A/C drain which was not a problem. If you taped up the air inlet, that would stop the rain comming in but would also stop the incomming airflow to the blower motor which would make the blower motor slave to try and move the air and would probably make it overheat and pop a fuse or burn up the motor its self. Im guessing that if you find that drain and clean it out your problems will be solved.
Im curious, did you have condensation (water) running in your floor durring the summer months? If so the drain is your problem for sure