I'm having problems diagnosing a P0301 code for 2010 Ford Fusion SE 2.5L 4 Cylinder?

About two weeks ago my vehicle began idling rough. It was most noticeable when reversing or at a stop light, otherwise nice and smooth on the freeway. I finally had a chance to check it out this past weekend and took it to Pepboy's and found the error code P0301 (cylinder 1 misfire). Since I had already planned on the maintenance I figured I could do the diagnosis along the way. First I replaced the spark plugs (with original Motorcraft), then I replaced EGR Valve (@ 250K it was about time)! In the process of removing the spark plugs they all looked good, no arching, tube leaks, etc.

The rough idle still continued. So I swapped the coils to check if the coil was the problem, and still nothing. Then I swapped the fuel injectors to see if the injector could be bad, and still nothing. Then I checked for air intake leaks, once using a compression test and another the old fashioned method of spraying carburetor fluid in the area to test idle, still nothing!

There isn't any smoke coming from the tail pipe as one would expect with an internal engine problem, so I don't think the rings are bad. I'm saving the engine compression test for last because it's the outcome I fear most! My thought at the moment is that the wiring to cylinder 1 could be bad, which I believe means replacing the entire harness. I know how to test the old fashion wiring, but how do I check wires for coil on boot?

Any suggestions on what my diagnosis could be? I'm going nuts here!

You forgot the one easy solution - replace the plug wires!

I guess gramps doesn't know about coil-over systems, anyway i would go ahead and do a comp test. If will iether give you the answer or elliminate that question.