"I don't know the condition of the vehicle when you brought it in."
That right there says a lot.
Now I don't know about other techs, but when I get a vehicle in wit an issue I make damn sure I know the condition of the vehicle so it will make sure that I don't do a faulty diagnoses..
Lots of guys will call a coil pack without even testing it,let alone test the compression or fuel system( other causes of a misfire condition
To me it sounds like the guy doesn't know his diagnostics and has some schleps working for him.

Take it to a reputable dealer ( save your tow receipts, rental receipts and so on ) and do like Mark said . Get pictures and documentation on everything.
If it proves out the shop toasted your engine sue him for the damages and let the dealer do the work.