I see a lot of people have looked at this, and nobody has replied.
I feel like I have the same problem in my 98tj, it's not that the heat is not working, it just seems to be slightly above temp. When you get into most cars, you have to turn the heat off, but maybe the soft top makes a huge difference.
I was thinking about it today when I was driving, because I remembered my heat working so well that I was commenting to people how amazingly warm it was. But maybe because that was in the fall, and not below freezing outside.
Check your blend door, it's located by the passengers foot vent. As you switch between hot and cold you should hear it or see it moving while moving the temp control.
Check to see if your getting flow through your heater core by getting the car up to temp and feeling both hoses. If they are both hot to the touch then your getting good flow, if they are just warm or cold then you have a clog.
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