If the door has been appart and the weather guard/moister barrier was not put back and re sealed to the door inner structure then this could also be the problem. The moister guard is a plastic sheet that is bonded to the door behind the door inner trim panel. Rain runs down the glass and past the felt channel and drains through the holes in the bottom of the door. Some of this water splashes off the glass regualtor and other components in side the door and ends up on the inner door frame. The moister guard is designed to funnel water back into holes in the door frame at the lower edge of the moister guard seal.

If the moister guard is not there or has not been re bonded it will let water puddle on top of the rubber weather stripping where the door frame seals to the cabin and with a good amount of rain it will spill/seep over the seal into the floor board. This type of leak is usually only seen when it has rained for long periods. I have had a couple of F-bodys with leaks like this, it took me a long time to figure out the first one.

Unless you have dealt with this type of leak before and know what to look for you would probably never find out where the water is comming from.