My car did the same thing when I first swapped in its second engine. Disconnect the negative battery cable, this will reset the ECU. Then start it back up, and once the idle starts to jump around, move the idle screw (on the throttle body, usually facing the driver-side fender) in and out a few times, and then set the idle to the proper speed. I don't know exactly why, but this almost always works to solve the jumpy idle.