You will need the assistance of a friend or relative, break out a garden hose, cover the cowl ventilation grill, sit inside the Jeep and spray copious amount of water on the header seal (between hard top and windshield) and inspect for water leaking in.
If no leaks found then perform the same test for the door seals and rear window seal.
If no leaks found then remove the cover from the cowl ventilation grill and test the cowl for a obstructed drain for the cowl drain.