Power or non power brakes really have nothing to do with the transmission (or power steering for that matter). (maybe your thinking along the lines of headers as they are affected by both above)
If you go power brakes, you will need a different brake pedal. Brake pedals are specific for power / non power applications.
You have two sources for brake conversion who are also members on this forum.
If you want to go with original, look up Dan of "Chockostang" Classic Mustang Disc Brake Conversions and Power Steering
Dan knows everyhting there is to know and do when it comes to brakes, steering for vintage mustangs.
You also have Dennis of "CSRP" Welcome to CSRP
He can set you of with conversion kits as well.
BOTH guys support their stuff and will help you with any question you have.
'66 Ragtop, vibrant red, 289-4V, 4-speed toploader
'68 Fastback, space blue metalic, 351C-4-V, 4-speed toploader
'69 Mach I, (Pending Resto Project)