OK I'm gonna try to decipher what you're saying:
-The ZC is NOT a D16a9, it is a ZC! If you were sold a "ZC" and it is stamped D16A9 you got ripped off buddy. I think that's a Euro engine from the Civic 1.6i-16 (I wish ours sounded that cool)
-You need to use the Si harness. The harnesses run in different directions.
-The wiring conversion at the distro is:
I THINK you have to convert the plug from the ZC distro to the one from the Si distro. Compare the wire colors: 2 whites, an orange, an orange/blue, a white/blue, a blue/green, and a blue/yellow on the old distro. The new one has all except the blue/green and the blue yellow. Change the wires (not the blue/green and blue/yellow) over to the old plug ONE AT A TIME, by pulling the pins, not cutting the wires. The 2 left over wires from the harness will run to the cylinder sensor on the end of the exhaust cam, closer to the front of the car. If you don't have a connector to use here, just splice the wires, but BE CAREFUL and use shielded wire.