Obiviously you have a rather large vacuum leak somewhere.
Will the engine run with the supercharger bypassed? If so, bypass it and see what happes to the vacuum problem.
There is no easy way to find vacuum leaks. It is a time consuming job that requires close inspection of each and every hose and connection.
Small vacuum leaks may not show much change using a vacuum gauge. The range of "good readings" varies so much from engine to engine that it may be difficult to detect small leaks. The engine in my first Mustang pulled about 16.5" of vacuum at 650-7250 RPM, which I consider rather low. It was a mass market remanufactured rebuild, so no telling what kind of camshaft it had. Average readings seem to run 16"-18" inches at idle and 18"-21" at 1000 RPM. The only sure comparison is a reading taken when your car was performing at its best through all the RPM ranges and what it is doing now. Use one of the spare ports on the vacuum tree that is mounted on the firewall near the windshield wiper motor.
Use a squirt can of motor oil to squirt around the mating surfaces of the manifold & TB. The oil will be sucked into the leaking area and the engine will change speed. Avoid using flammable substitutes for the oil such as propane or throttle body cleaner. Fire is an excellent hair removal agent, and no eyebrows is not cool...
The vacuum line plumbing is old and brittle on many of these cars, so replacing the lines with new hose is a good plan. The common 1/8” and ¼” vacuum hose works well and isn’t expensive.
Fuel injector O rings can get old and hard. When they do, they are prone to leaking once the engine warms up. This can be difficult to troubleshoot, since it is almost impossible to get to the injectors to squirt oil into the fuel injector mounting bosses.
Diagram courtesy of Tmoss & Stang&2birds
Vacuum leak due to slipped lower intake manifold gasket...
Ask Nicoleb3x3 about the intake gasket that slipped out of place and caused idle and vacuum leak problems that could not be seen or found by external examination. I don't care what you spray with, you won't find the leak when it is sucking air from the lifter valley. It simply isn't possible to spray anything in there with the lower manifold bolted in place.
See the following website for some help from Tmoss (diagram designer) & Stang&2Birds (website host) for help on 88-95 wiring
Mustang FAQ - Wiring & Engine Info Everyone should bookmark this site.
Ignition switch wiring
http://www.veryuseful.com/mustang/tech/engine/images/IgnitionSwitchWiring.gif
Fuel, alternator, A/C and ignition wiring
http://www.veryuseful.com/mustang/tech/engine/images/fuel-alt-links-ign-ac.gif
Complete computer, actuator & sensor wiring diagram for 88-91 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/88-91_5.0_EEC_Wiring_Diagram.gif
Vacuum diagram 89-93 Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/mustangFoxFordVacuumDiagram.jpg
HVAC vacuum diagram
http://www.veryuseful.com/mustang/tech/engine/images/Mustang_AC_heat_vacuum_controls.gif
TFI module differences & pinout
http://www.veryuseful.com/mustang/tech/engine/images/TFI_5.0_comparison.gif
Fuse box layout
