Ok lets see if I can explain this.
I have an 88 Vert and I have water coming into the car behind the drivers seat. Whats happening is where the top meets the metal behind the drivers windows there is a gap and I assume that there are holes for the water to drain out but its not. So its coming in the carpet behind the drivers seat. I tried to take a hanger and see if I could feel the hole(s) to unplug them but no success.

 

in those gaps there is a hole with a clear vinyl hose which goes through the floor board to drain