Sometimes the YJ develop leaks where the front of the door meets the body. Mainly this is when you have the "half doors" with the soft top on. An easy way to check it is to have a friend use a garden hose with the water on "gentle" and then go around the areas systematically. You should be able to tell where the leak is by watching for it on the inside while she/he pours the water slowly on the outside... one place at a time. I hope this helps.
Check out "YJ V6 Conversion" if you want to see a frame up restoration of my 1992 YJ.
Check out "WWII Jeep Photos AND Restoration of..." if you want to see the original JEEP in action...