Even though it's rare, sometimes you do get a bad part right out of the box. So, I would still go ahead and swap the plug wires side to side. Just crisscross them, pull them off the plugs and move them side to side. Your dual output coil fires both plugs at the same time. The cylinder at TDC on it's compression stroke uses the spark to fire, in the other cylinder it's just what's called a "waste spark". That means either plug wire can connect to either cylinder. So, if the problem follows the plug wire/cap and changes cylinders, it's got to be one of those two items. You could narrow it down even a bit further by then swapping the plug caps wire to wire.
You can also test the plug caps while they're off. I assume you've got the 5K ohm ones. Measure the resistance through them and see if it's right.