Carb to EFI conversions often suffer from electrical problems. That's the nice version of my opinion. Since you aren't the one to do the conversion, I'll spare you from the usual negative comments about such work.
The following diagrams will help get you aimed in the right direction. See the other diagrams for more on what the original 5.0 wiring was supposed to look like.
Ignition switch wiring: Note that there is a fuse link in the red/green wire going to the ignition coil. I do not know the location of it, but if you make sparks and smoke, it is probably blown open. Use a DVM or test light to confirm power to the red/green wire on the ignition coil. Measure between the red/green wire and the negative terminal of the battery.
Diagram courtesy of Tmoss & Stang&2birds
See the following website for some help from Tmoss (diagram designer) & Stang&2Birds (website host) for help on 88-95 wiring Mustang FAQ - Engine Information 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
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 94-95 Mass Air Mustangs
http://www.veryuseful.com/mustang/tech/engine/images/94-95_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
http://www.veryuseful.com/mustang/tech/engine/images/MustangFuseBox.gif
AutoZone wiring diagrams
For 79-88 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c1528004e28c
For 89-93 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c15280069677
For 94-98 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c152801f5e3b
For 1999-2005 model Mustangs
http://www.autozone.com/shopping/repairGuide.htm?pageId=0900c152801ef7d7