So you somehow applied the custom OS without realizing it but are also sure that when you did, you flashed it properly. Okay.
Another thing, a no-blinky from the 'noid light can for sure be because the ECM isn't sending a ground, but can also be no-blinky because there's no +12v IGN.
I think you are overlooking something simple yet fundamental, non-tune related. Wiring, missing +12v somewhere, connector pinout changed between the old engine and this one, etc. At some point you are going to have to crank up your diagnostic skills, or pay someone who's got theirs cranked up already.