Here's an image of our 3G "1-wire" setup.
http://www.wildhorses4x4.com/product/HiOutput_Alternator_130Amp
It doesn't show the business end, but it basically looks like any Ford 3G except for the missing Green w/red wire in the plug.
Some others that are also used are GM conversions. Don't have any pics of that, but I've seen some here over the years.
The way it sounds like yours was connected before should be just fine. Large wire between the main output post on the alternator, directly to the battery side of the starter relay/solenoid.
And the Green w/red from the Bronco wiring, to the Green w/red (sometimes just green) of the alternator.
Mustang's alts of this type would have been either a 2G or a 3G depending on what year it was sourced from. Obvious difference was the 2G had two output wires coming right out of the plug/connector, while the 3G had a single separate stud w/nut to connect the charge wire to.
Should be easy to determine a good exciter wire from the EZ Wire harness. If you're not sure about one or another, just check it with a volt meter to make sure it's only getting power when the key is on.
Are you at that point in the install yet? Or are you still putting things together with the harness and it's not quite ready to run yet?
Paul