It may be that the ECM is not powering up. If the ECM powers up, most any OBDII reader should talk to it, I would think so, anyway.

But given all you have done with the car, I'd not know where to start. Sounds like you'd changed RCMs, the battery, a ground cable and did I read that right - you changed the ignition switch assembly? Is everything plugged back in?
Have you measured to see if power is really getting to the ECM when you turn the key on? (Im thinking blown fuse or a connector somehwhere not plugged in all the way).