Rear end

The mustang rear could probably be used, as is. The explorer rear uses a long axle and a short one, and needs to be narrowed (probably cheaper than a mustang). You don't mess with flanges, you take a section out of thelong axle side, and use another short axle.
You would probably have to shorten your driveshaft and adapt for a ford size u-joint. Also, of course, remove the four link stuff off the mustang, and add new leaf spring pads. Explorer still uses leafs, but the pads will still have to be moved.
Unless you feel you NEED more beef, getting your 8 1/4 squared away is a better idea. Im gonna use an 8.8 explorer under my 57 chevy sedan delivery with a 454, in place of the plastic stocker. (NOT really plastic, but you get my meaning).