IF you are putting SN95 brakes on a car, you should mimic the SN95 brake setup completely. Don't cut corners.
The SN95 booster install is not that big of a deal. I honestly think guys overhype it. A careful approach and it slides right in. Hardest part is just screwing the 4 nuts back onto the booster from under the dash. Best method is to simply cut the studs down about 1/2" and slot the holes to the passenger side of the car. You don't have to touch the strut tower at all.
First off, if you are leaving the rear drums, don't do ANY MC or Booster mods. At the most, gut the stock prop valve and install an adjustable. There is no correct MC for the SN95 disks and rear drums...but stock might be fine because some of the caliper sizes are close to the size of the stock OEM caliper in terms of piston surface area.
Confused yet?
OK, well in terms of boosters, these are the boosters you want. 1993 Cobra, 94-95 ANY and 99-04 V6. 1993 Cobra will be the most direct bolt in, but only because all 4 studs match up. The SN95 boosters have one stud offset so you will need to drill that hole out. Performance wise they are all the same!
Which MC?? Well, keep in mind the 2-piston PBR's used on the 99-04 V6 used a 1.003" bore MC. The 1993 Cobra MC is also 1.0". SO, for that setup with Sn95 rear disks, a 1993 Cobra MC and SN95 booster (or 1993 cobra) will be ideal.
94-98 single piston calipers? you want the 94-95 GT MC 1 1/16"
94-98 cobra? use the 94-95 Cobra 15/16" bore MC
99-04 Cobra? 1993 Cobra 1" or the 15/16" Cobra for a little more sensitivity.
I get into more detail in the thread below on choosing your sizing if you wish to retain the stock booster, but i generally don't recommend it. The larger booster provides more assist, so you keep the stock booster requires more leg work. Might be fine in normal driving, but find yourself in a high RPM panic brake with low vacuum and you might wish you had the larger booster
this used to be stuck on top
Post #7 and #8 are what i consider the money posts