You need to be on the lookout for problems in the wiring going to the coil pack also, here's a good explanation of this that just came up today from BCZX3:
When you get a misfire in cylinder 1 and 4 as a pair (or 2 and 3 as a pair) it's usually indicative of an ignition primary circuit problem since the Ford "wasted spark" ignition system fires the plugs in those groupings. Of the three wires comprising the ignition coil connector, one of the two thinner outer wires should show physical damage, chafing, splitting or corrosion. (The thicker middle wire is 12V supply.)
Easiest thing to do is to simply tug on the wires; they usually break or come apart if bad.
If the problem is severe and persistent enough, eventually you'lll throw a DTC code - P0350, P0351 or P0352.