At least on my car which is a 1988 with a 3G alternator, the stator wire is connected from the 3 pin plug on the alternator, to the stator plug a couple inches away on the alternator. Stator is white and black, there is also a yellow and white that goes from the same 3 pin plug to the power terminal on the alt. Last wire way be your troubles, it is green and red and is the hot with key/instrument cluster idiot light wire. If that is not connected your alt will not charge. Of course your alt could be bad to.
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.