1994 Cobra, cutting off once operating temp reached

I have noticed that my Cobra runs a little rough. The car does have a tfs stage 1 cam in it and gt40x heads. Other than that it is stock. The rough idle I am told could be due to the cam and needing a tune. But the bigger issue is that once the car reaches operating temp and the thermostat opens the car has a tendency to cut off, run rough (motor bucks) and backfires through somewhere in the engine compartment when I hit the gas to keep the car running. And it wont start back up until the car cools back down. It cranks, acts like it catches but wont start. If I wait an hour or 2 go out and try again it will start. Any ideas on why this is? If more info is needed please let me know.
 
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