The Lincoln Versaille(sp?) rearend is the most sought after part in the world by classic Rustang owners. It's a 31 spline, heavy housing, with disc brakes and the small 5 lug pattern. Good luck finding one for a decent price, and then even more luck to you when it comes to finding a matching front axle. Are you swapping the front out too? If not, what about a 31 spline 8.8" from an Exploder? Same pattern as your factory front, disc brakes, and it's stronger than half of the 9" axles you will find in the junkyard. Most of them are new enough they won't need to be rebuilt either. The C-clips aren't a concern with rear discs.
If you want a 9", contact Currie for the best way to mount a modern and much more effective disc setup than ever came factory on any of them, which is the disc setup you will find on an Explorer 8.8".