There's a couple of ways to go about it. You can either use SVO/Lincoln Mark7 front rotors (same as a mustang but 5 lug) or upgrade to SN95 front brakes (requires spindle, hub, caliper, rotor etc). For the rear, again, you can use SVO/Lincoln Mark7 rear brakes and axles. This will give you disk brakes but will be about 3" wider than a stock Mustang rear and may cause tire clearance issues. Another option is to use Ranger axles and drums to keep drum brakes, stock width, but 5 lug. Finally, you can use SN-95 axles and brakes for 5 lug rear disks that are a bit narrower than the SVO/Mark7 pieces and a bit more modern.

The problem is none of this stuff is very common in the junkyards anymore.