Novak Conversions Jeep Wrangler JK shifters

Overheating

Your heater core is clogged if your not getting heat in the cabin which could cause the overheating.

I would still test for exhaust gas in the cooling system.

Not necessarily. An air bubble in the system will also keep heated water out of the heater core. Shutting off water to the heater core will not cause overheating. The OP had recent work done on his cooling system which increases the likelihood that there is air in the cooling system.
 
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I don't think the heater core is blocked. I will get heat in the cabin until it runs hot, then no heat. This is driving, when sitting the temp will slowly return to operating temperature and heat will return. I'm going to drain the system, change the thermostat and start with fresh coolant. I'll get the front end up with ramps and possibly get the spill proof funnel to get the fluid even higher.
 
I've read a few other how to things about flushing the system. I found that on my radiator I had to unsrew the plug all the way until it came out. A couple of YT videos state(show) turning the plug 180 and pulling out a little and the fluid starts to flow out the drain tube.
 
Thats a great clue. U are telling us that the heater works fine when the cooling system is working. That means the heater core is OK, and its not full of air. U also say when it running hot, you get no heat from the heater. If this is true, it sounds like it over heating because the coolant has stopped flowing. How can that be the case? If the T-stat sticks that could happen, the rad would not be hot. The coolant in the heater core could cool off, and the engine would be hot.
If u had a E36 BMW, I would say the impeller on the water pump could be slipping, but I think that's just a BMW thing.
 
Novak Conversions Jeep Wrangler JK shifters