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Join Date: Mar 2002
Location: Marble, NC
Found the below quote in another post on here, thought it would be useful...
Chances are pretty good that you should pull the heating system down, take it apart and reseal it.
There are 3 bolts that hold it on the firewall, you'll also have to disconnect the heater core, so drain about half your coolant first.
Taking out the passenger seat helps quite a bit with this.
Once you have it down on the floor, unscrew it, clean the halves well and then use generous amounts of black RTV between them. You'll notice that there is a hose that goes from a low spot on the heater assembly through the firewall and dumps out just under the battery tray on a YJ. If this is cracked, missing or cloged, you'll get water in your PASSENGER footwell.
If you're getting water everywhere, check to see if it's leaking out of the heater box, you'll see drips of water along the seam.