For my bluebird FJ20T I just plugged in the M4 pro with advanced tuning and got it to idle by cranking and richening the mixture till it fired and ran evenly.

I then pulled the map up at the next 500 rpm level, to the point where it ran evenly at all throttle openings and took it up in steps from there.

Once it was up to driveable rpm, On the road we just drove it and tuned as it was driven till the flat spots were gone and the mixtures seemed reasonable. That saved a lot of dyno time and money.