I can't say on the bellhousings, because you didn't state which engine was in the donor Mustangs.
The bellhousing issue aside, the main issue I see is converting the 2wd transmission to a 4wd transmission (assuming you are going to keep the Explorer 4wd). To convert a 2wd transmission to a 4wd transmission requires replacing the output shaft. The output shaft is the last thing to come out during a complete teardown, and the first thing to go back in while reassembling. Which essentially means that you are only the cost of parts away from completely rebuilding the transmission. I usually assume that, when someone asks about interchangeability, their goal is to avoid the cost/effort of a total rebuild. With that in mind, the answer is usually that it technically can be done, but it seems to me that it is essentially the same cost/effort as rebuilding your existing transmission.