Mine was a bit different since the later models used an internally regulated alternator. Something that may be of interest to you, I bought my alternator from Autozone (lifetime warranty) and IIRC, there was a new pigtail for the 3G in the box. Apprently there's an issue with the factory plug getting hot and melting so they ship the alternator with a new plug. I think in the end, since the 3G is internally regulated, you'll end up with the same arrangement I have. I have a 4ga. wire that runs from the alternator over to the solenoid on the battery side. I've got a massive slo-blow power fuse inline in lieu of the factory fuseable link.
I read a couple of articles on the swap and took the best ideas from each article and incorporated them into my project. The wiring was a piece of cake. The real pain in the ass for me was clearancing the lower bracket so the alternator would fit.
Check out this PDF file. It's all the wiring info you'll need. | 
1986 Mustang SVO Alternator Replacement 
