it's time to get out your voltmeter and familiarize yourself with the wiring diagrams...
The power windows use a circuit breaker mounted on the fuse panel. It only has power when the ignition switch is in the Run position.
The following are diagrams courtesy of Tmoss & Stang&2birds
Fuse box layout
93 power window wiring
See the following website for some help from Tmoss (diagram designer) & Stang&2Birds (website host) for help on 88-95 wiring; http://www.veryuseful.com/mustang/tech/engine/ Everyone should bookmark this site.