The engine speed is controlled by the amount of air entering the engine. There should only be four ways for this to occur, the throttle plate, the idle speed adjustment on the top of the throttle body, the idle valve, and cold idle bypass valve. When the engine is cold, it should idle around 1500 RPM and slowly drop to about 850 when warm.
Few questions, when you changed the plugs for the TPS, VAF, and ECU, did you splice the wiring or did you pull the pins from the original plugs and put them in the new ones.
Did you wire up the variable intake solenoid? If you didn't yet, I would use the Blue/Orange wire that went to the Barometric sensor(no longer used) and just extend it to the solenoid plug and connect the wire to C205-pin S. It activates around 5000 RPM and adds an extra 5 HP.