You brought in a severely overheated engine. The shop doesn't know about the coolant your Jeep requires. You have a random cylinder misfire, which means it could be one or many cylinders but the system doesn't know which ones specifically. And with having a misfire code and feeling the misfire when driving, the shop isn't telling you anything? Did they send you on your merry way like this? I sure hope not. If so, you need to take your Jeep anywhere else but there. Given the circumstances (overheating), you could have anything from a blown fuse to a blown head gasket. (let's not over analyze the fuse suggestion, it was for demonstration purposes only). Knowing what happened, the shop should have done a combustion gases test on the coolant, a coolant pressure test, and perhaps even a cylinder compression test. Your possible causes for the misfire are many.
The shop did tell me about the cylinder misfire code and that it felt that way when they drove it.
It was my choice if I wanted them to further diagnose the cause for additional charges or if I wanted to take it home today after the water pump and thermostat were replaced along with the coolant flush with HOAT.