Another option is to use a commercial flush product. Drain the coolant, add distilled water and flush solution, and then give the Jeep an Italian tuneup (run it as hard as you can for a while). Drain the flush mixture, rinse with distilled water, and refill with water/coolant.
However, it also could be unrelated to the heater core. If the blend door isn't fully closing off the flow of cold air, it could result in cooler air from the vents. Only real way I know of to fix this is to pull the dash, which is a lot of work