If it was me, I think I would go back to the basics. You have reprogramed 1 computer, and then replaced it and the harness. Although it's not impossible for that to still be the problem, I think for the time being I would rule it out.

Don't know if you've done this yet, but I would look for things like a faulty sensor, connection, wiring problem to include grounds and proper voltages. I would also not ruile out something as simple as an intake manifold leak.