I found the best way to clear the drain is to remove the cowl cover (between the hood and the windshield on a TJ) and physically remove the debris which are blocking the drain at the bottom. If you simply run a wire up from the bottom of the drain you can remove some of the garbage but it will plug up again (especially if you deal with lots of mud). It wasn't hard and should eliminate the problem for a longer period of time, note when the cowl drain becomes plugged it will submerge your windshield wiper motor (on a TJ)- not a good thing.