99 WJ only blowing air, not getting hot or cold
 

Anyone have any ideas why this would happen? I tried swapping the control unit with no luck. It did have the same issue every cherokee had with the resister/module overheating and melting the prongs etc. I fixed that. But now it's just "air". Won't get hot. Won't get cold. Fuses look ok. Everything seems plugged in and ok. Has anyone had this same issue? Or know a fix?

Most likely the blend doors...
You can get a repair kit - the fix involves carefully cutting a hole in the side of the heater box to replace the broken / faulty parts.
Not too difficult to do - had to do mine a while back.
Repair kit is not too expensive.

You can check the blend door. Take out the glove box. You'll see the heater plenum behind it. You can see the pivot point for the blend door. Its like a door hinge. Twist it, like up and down. If you can feel the door and hear it moving up and down , it's okay. If it feels stuck , like you can't even move the end of the hinge, its jammed up. Or there is play in it the hinge is broken. You can go to the Heater Treater web site and follow the diagnostics. There is another site that escapes me right now, Doorman also sells a repair kit on AMAZON. Lots of options for repair.

You forgot to mention there is a stepper motor mounted over the end of the shaft. The shaft is plastic and breaks easily. When you remove the motor, it's obvious if the shaft is broken. Dual zone heaters have 2 doors and the one in the rear requires removal of the dash.