If you have the 350Z harness and ECU, I would go that route. The time it will take you to build a MS harness, debug it, tune it, etc. is not worth it. In the end you have something that will never run as good as a stock 350Z. Those Nissan engineers are pretty sharp, and they spend way more time on a dyno and test track than any of us ever will.
Also, if you disable the variable valve timing you will loose that nice flat torque curve the VQ35 has. Again, Nissan has done the work for you,.
Sell your Megasquirt and pickup a 350Z ECU and harness.
Pete