The cluster gear transmits power in every gear except 4th. You may have a problem in that area.
Diagrams courtesy of Tmoss & Stang&2birds
T5 Cutaway showing T5 internal parts
I don't know how you feel about the DYI thing when it comes to gears, some people don't like the idea of working on transmissions. If the DYI transmission fix idea isn't something that you would rather leave to someone else, here are some resources:
See
http://www.ttcautomotive.com/English/onlineorder/product.asp to download a FREE service manual for T5 or Tremec 3550/TKO
You will need the Adobe Acrobat viewer which is also a free download –
http://get.adobe.com/reader/
See
http://www.hanlonmotorsports.com/ or
http://www.ddperformance.com for parts
A T5 rebuild kit with syncros, bearings and other small parts costs about $160. It does not include any gears or shafts.
http://www.hanlonmotorsports.com/ also has a video on how to rebuild your T5 or Tremec. It costs about $20, and is worth every penny of it.
I did a Tremec 3550 rebuild, and it wasn't that difficult. The video was an immense help, and I would recommend viewing it. At $20, it will give you an opportunity to look and decide for yourself if you think that it is something you want to try to do.
T5 Shim kits – best product I have seen in a while…
http://www.5speeds.com/t5/shims.html
“The Peel ‘n Place T5 World Class shim kit makes shimming T5 counter gear and main drive gears very easy.”
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.
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
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_Guide.jpg