3 things are needed for cylinder to fire
1. fuel, in the right mix with air
2. spark, at the right time and strength
3. compression, above 120psi
Compression will be taken off the table, for now
Fuel pressure, as adsm08 said, would tend to effect more than one cylinder
Fuel mix from partially clogged injector could effect under load operation only
But I would expect higher speed highway driving, light load flat ground, to also be effected.
Spark, when accelerating fuel mix goes very RICH, so spark needs to be strong or it can't ignite the mix.
Each coil in coil pack sparks 2 cylinders at the same time, while it would be possible for only 1 cylinder to be effected it is a long shot.
I would first switch spark plug wires on #2 and #3, or any similar length wires, see if issue moves to the "other" cylinder
Next pull out #3 spark plug, check it's gap, 0.054 is a big gap and 4.0l needs it to get a good strong spark, if you can replace it with 1 new spark plug, or swap it with #2 or easier to get to spark plug.
If spark doesn't seem to be the issue then you will need to move on to #3 fuel injector
Coil pack wiring
3 4
2 6
1 5
front
The 5 6 4 side gets me