After this work, you have:
-Eliminated spark concerns (spark plug testing good = plug, wire, and coil are ok.
-Eliminated fueling concerns (confirmed injector pulse signal = PCM knows when to fire cylinder #4, replaced #4 injector)
The fact that the misfire is concentrated on a single cylinder means timing isn't the issue, so we can rule that out.
Short of some freak electrical problem, this diagnostic path seems to be leading us down the mechanical path.
What is the compression like on #4 compared to the other cylinders?
A flat cam lobe can prevent the valves from opening or sealing properly. Did you inspect the cam lobes when you had everything apart?
A cracked valve spring may not have the amount of spring pressure required to properly shut the valves and seal the cylinder. Did you inspect the valve springs on #4 when you had the head off?
Also, just out of curiosity, is this engine a fixed Atkinson cycle design or variable? (can switch between Otto and Atkinson)