I did the same (running MS after failing to tune the Neo / fmu).

I am in the process of making videos of my install, search "Evan's Megasquirt Build" on youtube if you are interested. I'm still new, but I'm making videos as I learn things.

In the process of switching to MS, I realized I had a bad injector, which was probably throwing off my ability to tune it all in with the stock ECU, but I got the car with MS in mind anyway, and I'm well on my way.