Disconnect the fuse links and see if you still get a spark.
Fuse links come with a current rating just like fuses. A clue as to what current they are designed for is to look at the size wire they protect.
Typically it is something draining the battery. Small things like glove box or courtesy lights are often the culprits. If you have an aftermarket stereo or alarm system, it is also suspect.
The ideal method is to disconnect the negative terminal, and connect a Digital Multimeter (DVM) between the negative terminal on the battery and the negative cable. Set the DVM on a low current scale of 2-5 amps if it doesn't auto range. Watch the current draw, and then start pulling out fuses. When you see a sudden drop in the current, that circuit is the likely culprit. Note that the computer, radio & clock will draw less than 1/10 amp to keep the settings alive.
See
http://assets.fluke.com/appnotes/automotive/beatbook.pdf. You will need the Adobe Acrobat viewer which is also a free download –
Adobe Acrobat Reader DC Install for all versions
If you can’t find the current drain by pulling fuses, then the alternator is suspect or any aftermarket sound or lighting equipment that may be on the car. Disconnect the alternator output power plug, then disconnect any aftermarket sound or lighting equipment while watching the current on the DVM.
Diagrams courtesy of Tmoss & Stang&2birds
Fuse box layout
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.
94-95 Mustang wiring diagrams
Mustang FAQ - Wiring & Engine Info
Complete computer, actuator & sensor wiring diagram for 91-93 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/91-93_5.0_EEC_Wiring_Diagram.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
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
O2 sensor wiring harness
http://www.veryuseful.com/mustang/tech/engine/images/mustangO2Harness.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 & pin out
http://www.veryuseful.com/mustang/tech/engine/images/TFI_5.0_comparison.gif
Fuse box layout
http://www.veryuseful.com/mustang/tech/engine/images/MustangFuseBox.gif
Mustang 5.0 Lights and Radio schematic, by TMoss:
87-92 power window wiring
http://www.veryuseful.com/mustang/tech/engine/images/mustang87-92 PowerWindowWiring.gif
93 power window wiring
http://www.veryuseful.com/mustang/tech/engine/images/mustang93PowerWindows.gif
T5 Cutaway showing T5 internal parts
http://www.veryuseful.com/mustang/tech/engine/images/5_Speed_Cutaway_Illustrated.jpg
Visual comparison of the Ford Fuel Injectors, picture by TMoss:
http://www.veryuseful.com/mustang/tech/engine/images/Ford_Injector_