I used mostly stock 4.6 wire harnesses forward of the firewall and connected them to the dash wiring ('88 Mustang dash in a '79 Futura). The only modification to the harnesses were for four headlights and I moved the battery to the trunk. Your '85 should have a U-shaped harness that goes down both sides of the engine bay and plugs into the dash harness in the center. Probably the cleanest way to connect to the 4.6 would be use the large connector that plugs into the center of the dash and make a harness that connects the dash to the 4.6 wiring. The link in the previous post will direct you to the wiring forum, and when you open it, the top thread will be my general discussion on wiring a Modular engine. It contains a sketch showing the connectors that mate to the dash on a an SN-95 Mustang and the interconnections between the underhood harnesses. My friendly local salvage yard let me cut the mating connectors to C105, C107, C 213, C216, and C259 from a wrecked Mustang. Make sure you leave the pigtails long enough.
Making a harness is not difficult, just tedious, and my advice having been there and done that is to figure it all out on paper before you start cutting wires. If you don't have it, get yourself a good ohmmeter. And if you need wiring diagrams, send me a PM. I have '96-'98 wiring diagrams in book form and on CD, and 1999-up also on CD.
