b&m makes all sorts of shifter that fit in the center console for mustangs. You put them in the console and they come with a nice top cover plate and a boot for the shifter handle.
you can rig one of those big ass ratchet shifters in there, put sheetmetal over the hole to mount the shifter itself. as far as the console you can use a heat gun to mold the shifter cover to the stock console. Its afro engineering but can be done