Some information within online service manual we have access to. Unfortunately it's important wording is incomplete. We used to have better access.
Glass must be removed first, then regulator.
Two bolts and sleeves retain glass. "Tip the front of door glass down to clear door filler and remove the window glass." Ford Workshop Service & Repair Manuals - 2005 Mustang Glass, Frames And Mechanisms Window glass front door Ford Workshop Service & Repair Manuals - 2005 Mustang Glass, Frames And Mechanisms Window regulator and motor front door
"Remove the door glass...Disconnect the window motor electrical connector. Remove the three window motor nuts. Note: Make sure not to disturb the jack screw when removing the lower right window regulator nut. This may affect the window adjustment.
Remove the four door window regulator nuts.
Remove the door window regulatory and motor through the rear access hole.
After installation of new motor/regulator adjust the window glass as necessary."
The real service manual has details on adjustments and initializing a new motor.