Mark 7's have hydroboost setups. Typically those offer more boost than vacuum boosters so I wouldn't change that out just yet.
There's no ideal MC here as your setup never came factory on a car. You'll need to do a little math to figure what is the best to use.
So your stock setup would be:
SVO calipers: 73mm piston
-8370mm^2 for 2calipers
SVO REAR calipers: 54mm piston
-4580mm^2 for 2 calipers
Giving you 12,950 square inches of slave piston surface area as a stock Mark 7 setup
Now, you've changed to this
99-04 COBRA 40.5mm pistons
-5152mm^2 for 2 calipers
SVO REAR calipers: 54mm piston
-4580mm^2 for 2 calipers
Now giving you 9732 square inches. If you ran your stock 1 1/8" MC, you'd have a hard pedal.
So lets look at the 94-95 GT setup which uses a 1 1/16" MC which is the next smallest size down.
94-98 GT/V6 calipers : 66mm piston
-6842mm^2 for 2 calipers
94-04 rear calipers all : 38mm pistons
-2268mm^2 for 2 calipers
That's 9110 square inches of total piston surface area using that 1 1/16 MC.
That's not too far off from the setup you would be running. I'd leave the MC alone for now and try this MC instead. Of course, undure if it will physically bolt to the Mark 7 hydroboost setup. I'm assuming yes? Not a common brake setup you are going with here, so you might have to play around with it
My info came from here if you want to play around with numbers a bit yourself
https://www.stangnet.com/mustang-fo...onversion-upgrade-thread.801400/#post-8075734