I've seen a few threads about inadequate heat in some TJ's, mine had a problem with low air temp. I checked the blend door as was suggested in some posts & it was working good. Pulled the heater hoses off & tried flushing with a garden hose, I barely got a trickle through it. I went to the local hose shop & bought some fittings to back flush it using air and water. Wow, what a difference! Looked like mud coming out for a while! Now I've got great heat!
Here's a pic of the setup I used. Garden hose fitting at the top, blow gun on the right and 5/8 hose barb to hook to the heater hose. I used the blow gun so I could regulate the amount of air I was putting in (plus that's what I had handy!). Cost was about $15.