I don't know the pattern on the Z31 chopper wheel but I know on3go had some problems with his z31 chopper wheel when he was switching over to MS from SDS. I ended up selling him my 83 turbo dizzy and that got the thing running.
Opinions... I would say go the route most traveled. That includes MS I (although I have had a smooth experience tuning and helping setup a MS II powered Z) PCB v3.0 and a relay board to help you rip out all the old wiring. Use the 83 turbo dizzy, and run ignition through an MSD, High current coil driver (VB921) or gm hei module. Any of those choices will be faster than seting up any COP or Waste spark system.
Unless, of course, you're up for the challenge of seting up a complicated ignition system.
If you have already attempted swapping the 300zx ecu into your car, then you have at least had a crash course in setting up ECU's. That should be more than enough experience (along with all the help you can get here) to setup your Megasquirt.
GL
-Oliver