Hey guys, I worked as a service Manager for Toyota for about 8 years. The problem you are having is common after it rains. The ONLY thing I have ever seen be the issue is, the water gets trapped in the Running Boards. These are the steps that you use to enter and exit the truck that run along both the left and right side. The rubber plugs are on both front and back ends undernieth the running boards. You will have to get on your back inorder to see them. Not a difficult task at all and this will solve the solution. Just pull them out. If it doesn't help then there may be something inside the boards clogging the drain hole. I would then toss the plugs or do what you wish with them.