Well I edited the post a bit and corrected spelling, and I have read it 6 times. I see a lot of stuff that isn't relevant and still wondering why you are waiting with a radiator cap in your hand :>)
So you had a lot of coolant leaks, you have them fixed and you were worried about the water pump, so you told them "while you have the car up on the hoist for the wheel bearings, change the pump please". They did that, they lost a fixing bolt, but they found another. Now the car misfires.
Well the water pump and the coolant system don't affect how the engine runs. The only thing I can think of is that when they changed the water pump they disconnected some wires that were in the way of the pump. Maybe the Crankshaft Position Sensor is down there and wasn't connected firmly.
Shops shouldn't be charging $280 for plugging in a scan tool, my tire guy does it for nothing, having said that, the Lexus Dealership charged my $238 for a $40 plain wheel bearing!
The water pump is not easy to get to
https://www.google.com/search?q=2012+CHRYSLER+200+TOURING+replace+water+pump
Just seeing where the CPS is
https://www.google.com/search?q=2012+chrysler+200+touring+crankshaft+position+sensor+location
Misfires should display a code
https://www.google.com/search?q=2012+chrysler+200+touring+misfire
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