Fair enough.
So just to clarify I seriously doubt anything is wrong with the ecu or tps. The main thing you have changed that will upset the ecu Is the throttle body.
Maybe the ecu sees alot of air running through the engine even though the tps is at .4 volts and doesnt believe the car is at idle. Can't you look at the idle control valve duty cycle? I bet it's really low, or off all together.
I'm betting it's the throttle, assuming you have no leaks, but if you choose to ignore that it's cool with me.
Email matt at nistune and ask him what conditions have to be met for the idle flag to be raised. We know that the voltage is one, maybe there are more.