OK, so you are confident that the coil, plugs and HT caps are all good for both sides? The HT side is complete.
So working backwards the problem is on the LT side of the supply to that particular cylinder...check back thoroughly again, all the connectors and blocks between the PGM and the coil.
Check continuity but also see if you can measure resistance values and compare each side.

As a thought have you checked for plain old supply voltage to each side when running/kicking over?