I'm new to the group and have a 2008 JK, we recently replaced the thermostat after we had a boiling over issue. Now the heater is only blowing barely warm air, any relation? Thanks for any help, seems like it might be a related issue since it boiled over again the other day when I left it idling for a while to charge the battery. Temp gauge is normal

 

A couple thoughts: That might happen if it wasn't filled properly with coolant and is quite low. The way I fill and burp the air out is to park on a hill, front high, and fill slowly. Fill the reservoir about half way, then check/re-fill every cold start until the level stops dropping. Generally I like to see it about 1/3 full cold after all the air is expelled.

Do you have the old thermostat? Was it tested? To test the old thermostat, put it in a pan of water on the stove and bring the water to a boil. It should start opening at ~195F and be full open at ~212F if I remember right -- You don't really need a thermometer for a functional test, just boil it and watch it open. Bottom line is to be sure that the original part was actually bad, and the real problem is something else.

Side note, I usually boil new thermostats to check them (in the same pot with the old one). I've seen a couple bad ones right out of the box.