I’m assuming you checked all the sensors and harnesses that were near the motor mount you changed. I’m not sure if this helps, but here is a list of the inputs to the idle air system:
Camshaft position sensor
Mass air flow sensor
Engine coolant temperature sensor
Throttle position sensor
Park/neutral position (PNP) switch
Air conditioner switch
Power steering oil pressure switch
Vehicle speed sensor
Ambient air temperature switch
Intake air temperature sensor
note this is from the 2003 Frontier FSM, but I don’t think the VG33E has changed much since then.
Are you able to look at live data and see what the desired idle is? Can you look at freeze frame for the P0100 to see what may be out of spec?