The Gen 4 uses an idle speed control valve in the throttlebodies to control and adjust the speed. If the second set of TBs is doing the same thing, then the question is if the control valve was reused from the second set? Or did the second set of TBs come with it's own?
Sounds like the control valve is bad. Or the wiring that goes to it. Or the ECU that controls the valve isn't providing the proper output. ECU reflashed? If it's not, then you likely have a wiring issue from the ECU to the control valve.