Wiring confusion MSD 8388 Distributor to a new harness

Your link to the harness did not work, but I assume it's a repop harness with the ECU wiring built in.

You won't need the ballast with that. I would be tempted to carefully unwrap / cut open the harness and remove the ECU wiring. You might even sell it here for a buck or two.

Hook all the wires going to the ballast together, except the ones leading to the ECU plug

Use the original harness coil + wire to feed to your coil +

If you are careful, use good crimp or solder connections and heat shrink, you should be able to "hide" all that in the harness when re-wrapped.