Hmm, This is a toughy. I think the first thing you should decide is what do you want to do with the car? Are you looking for a driver,a race car(Round track),a Drag car,a show car,etc?I assume you're building it to keep? What general type of budget are you looking to work within?
That said The explorer rear. Most people that I know who have done it have done it as a reasonable way to get rear Disc brakes and a posi rear with good gears (most of the choice ones had 3.73 posi's).They don't do it to handle high horse power.If you were building a drag car you wouldn't want to go the explorer route,You'd want to go with a 9 inch,Believe it or not you could do pretty well with a properly setup 8 inch as well.
Next area buying a full size car or truck and swapping. First area 460 engine in a 66 Mustang You would need to remove the front shock towers so now you're talking major fabrication and work I.E. A Mustang 2 coilover setup or a Fat man fabrications setup,etc. This is a lot of work to install a motor that was never really meant to be a race motor,I know it can be done but it will never be an F.E.. Additionally a 460 in the front of a 66 Mustang will make it wallow through the turns like a pig.
Next area full car/truck The transmissions in this vehicles were more often than not Autos,They're weren't all bad some of them had C6's which are strong trannies but they are also heavy and Full size Fords use Larger transmissions that have Long tailshafts and tailshaft housings That pose install problems into early stangs.Truck trannies usually pose the same problems but to the other extreme alot of the trannies were shorter depending on what type of truck,van,4wd,etc. The next tidbit to address would be the rear,Most of these vehicles used 9 inch rears (Yay) Which are virtually bullet proof,However Fullsize Fords were changed over to coil spring rears in the 60's and trucks were leaf which is fine but the spring pads are placed too far apart and the the rears are typically too wide to fit into a 66 Mustang.They do however all have center sections that you could use depending on how many splines they are (28 or 31).
Although I prefer stock or stock appearing cars,I've seen alot of different types of builds,I also have some reference pieces, Currently I own two Full size (big block,nine inch rears,etc.)60's Fords .Additionally 3 of my 65-66 Mustangs have nine inch rears in them currently.I'll be installing nine inch rears into 2 of my other early stangs at some point (who knows when?LOL) as well.
If you get a chance I'd love to hear more about your car(Is it a 6 or an 8 cylinder,etc.?) As well as your thoughts as to where you'd like to go with it? Perhaps I could help give you some ideas as to what you could use and where you could find it.