Idle Speed. What makes it right?

Just remember that whatever the manufacturer's did was after months or years and lots of money R&D.

You, that is we, have created a completely new and unique engineering prototype with any custom engine build

"What might be easier" would be to revert to carb and dist to optimize it, then measure AFR and look at timing so you know where you ended up

The way I see it the big stumbling block is there is no "knobs" in the software like screwdrivering the carb idle mixtur, or grabbing the distributor "bodily"
“Knobs” or idle mixture screws and jets have been replaced by strokes of a key board. While some people are less apt to embrace that kind of change, I will say once you learn it, it’s much easier to hit a couple keys and make changes than it ever was getting out a screwdriver and turning a “knob”. With the correct sensors every single change you make happens in real time and you can watch what each one does. Maybe not so much on the sniper/fitech type of efi systems where your just plugging in some engine parameters and letting the ecu self tune, but real multi port efi.