Multiple Random Cylinder Misfires, Cylinder One Misfire

A month ago the engine started running a bit rough, hesitation, rough idle, power surges- at a stop it would feel as if it were going to stall out- never did stall out. I took it to a mechanic, was told it needed a tune up, an ignition coil on cylinder three, set of spark plugs and a new egr valve. All checked out with my research and I decided to have it done.

Within a day of being fixed it started to have the same issues. This time they were stating that cylinder one needed a new coil. I was tired of paying out cash at this point, decided since I was going to perform a brake job, I would replace all of the remaining coils. Pulled the plugs and despite being new they all had a very dry carbon deposit on them. Cleaned off the plugs. Changed out the three coils that had not yet been replaced. Drove the car around, and it was fine for about six hours, the engine cooled off and suddenly when starting it threw the same code. Engine was rough, power surges, stuttering. Cylinder one was still misfiring. So to trouble shoot it, I took the plug from cylinder one and put it in cylinder two, took the coil from cylinder one and swapped it with cylinder three. At the same time did a fuel system clean out, thinking maybe it could be the injector. Suddenly the car road well, all while the engine is warm, shifted normally, no power surges, no issues. Did an oil change, put 0w 20 full synthetic in, replaced filter, etc.

I'm still having the same issue- when I start the car cold it has the same issue, misfires, stutters and surges- however when the engine warms up it seems to be perfectly fine. I can clear the code while the engine is warm and it won't come on again- tested it, drove three hundred miles to Miami and the car didn't throw a code once- it did throw the code when I started the car the next morning.

A slightly new issue- my MPG have gone down- from about 20 MPG highway to roughly 16-17 MPG. I'm not entirely certain which avenue to head down next.