I had the same water leak in my 93 YJ. The vent on the cowl will fill up with water if the drain tube is clogged. If your screen under the vent grille is bad, it will allow leaves and debris to clog the tube. Water will fill up and then come in through your heater ducts... sometimes dousing your left leg real good when you make a turn!
Take the grille off and clean out any debris you can see from the top and fix the screen. Under the hood, you will find a black rubber drain tube about 1" diameter close to center at the firewall. The tube is crimped flat at the end and has a piece of spring steel in the end to keep it closed so you are not sucking engine compartment fumes into the passenger compartment. Sometimes, you can just squeeze the end and the spring steel will allow the tube to open up and dump its' contents. Usually, the rubber tube is old and stiff and the spring steel doesn't like to flex. In this case, you may have to go underneath and stick a long flat screwdriver into the tube to clean out the debris and open it up. CAUTION: If there is still any water in there, it WILL run down your arm, so plan accordingly! BE SURE TO WEAR SAFETY GLASSES TOO!
You may wish to check your handywork with a garden hose to be sure the drain flows freely after you're done!
Hope this helps...