On my 97 TJ the door that controls the door for heat/cool is controlled by a cable, vacuum controls where it comes out though. There is a cable that comes out from behind the dash on the passenger side, on the left side of the passengers foot area, above where your left foot would be when you are sitting in the passenger seat there is a cable that is attached to the arm for the flapper. On my old TJ the part of the cable that is attached to the outer sheath which then attached to the heater box was broken and so the flapper door didn't seal all of the way, when you turned the blower on hi the pressure would push the door a little so you didn't get full heat, I repaired the clip on the outer sheath and my heat seemed to be a little hotter. I am not sure this is the same problem you are having but it helped mine. Flushing your heater core is a good thing to do anyhow, I would start by putting the hose on the output to dislodge anything in the core, but I would flush in both directions.