waste spark pair
Plug #3 and #5 fire at the same time in your waste spark ignition system. Therefore, a problem with either plug or wire will affect both. Since you have replaced the plugs, wires and coil I agree with SoNic67 that you may have a problem with the trigger signal electrical path from the PCM to coil #2. You may want to disconnect the PCM connector and check for continuity from PCM pin 52 (red/light blue wire) to the connector that mates with the coil. Also check for isolation from chassis ground (not shorted). You should also make sure that pin 52 does not get pushed back when the PCM connector is installed.
The causes for engine misfire are ignition, fuel injection, and compression. Only ignition matches cylinders #3 and #5.