2005 Ford Escape Replacing Powertrain Control, Wire Harness

My car would not start the Saturday after Thanksgiving. I had it towed to my dealership which has been servicing my car for the last several years. I was told the the computer/Powertrain control module had died and also fried some of the wiring. The part took almost two weeks to get to the dealer. They have put it in along with the harness. The quote for this work was $1916. This included two hours of diagnostic work. After putting in the parts they have found that the car is only running on two cylinders and the four of the coils need to be replaced. They are recommending all six coils be replaced along with the spark plugs. New estimate is $3020. Does this sound legitimate?