Set it on a flat surface, perferably like a slab of glass, or a glass table. It should be pretty obvious if its warped or not. You could also have a hairline crack that isnt visible to your eye. I would say check for flatness, and use a light amount of RTV with a new gasket and tighten to spec. If it still leaks, replace the housing.
You never said the year of your Jeep... is it a RENIX by chance? If so its very likely that you have trapped air in your system causing the no heat condition. If your 91+ that shouldnt be an issue.
I also am assuming that you flushed your system before you installed the new thermostat?? You didnt state that. If you did, its possible that during the flush you pushed something into your heater core and now its clogged up. You want to flush your system as a whole FIRST, then flush the heater core. If its all connected, an easy test is to touch both the lines close to the heater core and see what temperature they are (when the engine is at operating temp and being CAREFULL) If one of the hoses is hot ( i believe the top one will be hot) and the other is lukewarm or cool to the touch, then your heater core is the prime suspect.
I hope that helps.