When replacing the HU in the new mustang your also removing the sync system. You have to get a replacement dash kit which actually comes with an opening for a double din deck an the new heating and a/c controls. IMO i would keep your stock head unit and add a couple of amps. A 4 channel amp for your mids and highs and an amp for a sub. 2 12 requires a pretty decent size emclosure, i remember delivering a dual 12" box toy buddies house and it wouldnt fit in the trunk or the opening with the back seat down. I had to fold the back seat down amd place it ontop of the backrest. Your best bet id maybe going with a singal 12" enclosure seeing as tho you already have the drivers, or a custom enclosure depending how deep your pockets are.
hope this helped dude