The problem may have nothing to with the new Master Cylinder or old diaphragm.
Are you getting a hissing sound?
It could any number of other reasons for the high idle.
But the Jeep in park, at idle, cold and later warmed up, try cold and hot states.
Press the brake (while in park) and see if the Idle jumps.
If it does run up the idle, disconnect the large rubber vacuum hose attached to the Vacuum Booster and plug the hose end so air can NOT get sucked into the intake manifold.
If the High idle problem stops, it is the vacuum booster.
If the high idle does not stop it is wiring, connectors or sensors, like the brake switch under the dash not telling the AW4 transmission computer to unlock the Torque converter, or a ground issue in the wiring...or TPS Throttle Position sensor or or ground on it.
Tell us what your find please. Good hunting