I did it the same way you did. When I threw it up on the saw horses to complete the welding, it hit me that I did a bunch of extra work, laying on my back for nothing. And to make matters worse, this is the third time I've done this type of modification. Guess I'm a slow learner.
It would be so easy and cheap to make a jig for this. All you need is a couple of fairly straight 2x4 studs, the use of a table saw and a couple of saw horses.
I'd measure the '86 drive shaft just in case. Although I think xoxbxfx is right, the SN95 does has a longer input shaft and bell housing, but definitely not by 4". So the Fox driveshaft probably is too short. That would suck!
As for quad shocks, you'd have to find some very lightly valved shocks to run quads on an early Mustang. Not a whole lot of weight back there, unless you build an Explorer rear end
That brings up another point. I bagged pretty hard on the Explorer rear end, and it started me thinking about why there is such a difference in weight. With the 3" axle tubes and extra heft (disc brake crap aside), the Explorer rear end might be able to handle more torque than a Mustang 8.8. Unless Ford beefed it up just to handle the excess weight it (and the Ranger for that matter) would carry. Still though, if you're running a T5, it ain't the rear that's going to break from too much power.
So I'm sticking by my previous post that the Explorer differential and it's associated disc brake setup is a big fat pig... with no ears
YMMV,