The stock master cylinders on the 87-93 Mustangs are marginal with just the install of larger front 73 calipers. The 3 port design is really to blame with the small 21mm bore. If you swap to rear disc, then a new MC is needed! There are 4 common MC upgrades out there for the Mustangs: the Lincoln/SVO unit, the '94-98 V6 unit, the '93 Cobra unit and the '94-95 Cobra units. Each is a 2 port MC, so a conversion will be needed but they are all different bore sizes. Which one is the correct unit for you? Read on:

Here is a more specific information on the master cylinders mentioned:

'84-86 SVO - (SAE Threads) 1 1/8" bore, old style aluminum reservoir unit. no low fluid sensor. This is the same as the 84-90 Lincoln Mark 7. The difference is usually the SVO is aluminum, and the Lincoln can be a cast iron unit. The aluminum is what you want to keep the weight down.
'85 Towncar - (SAE Threads) 1" bore, old style aluminum reservoir unit. no low fluid sensor.

'93 Cobra - (metric threads) 1.00" bore
'94-95 GT/V6 - (metric threads) 1 1/16" bore, stock plug in for the low fluid sensor
'94-98 V6 - (metric threads) 1 1/16" bore, stock plug in for the low fluid sensor
'94-95 Cobra - (metric threads) 15/16" bore, stock plug in for low fluid sensor. Ports are reversed thread sizes from 87-95 LX/V6/GT
'99 V6 - (metric threads) 1.000" and 1.006" bore. Can be converted to work for the low fluid sensor on the fox3 cars
96+ V8 Units - These are hydroboosted and the mounted flange is vertically vs horizontal required for a vacuum booster. They will NOT work

Low fluid sensor notes: The stock '87-93 master cylinder has a plastic reservoir with a low fluid indicator. The '93 Cobra and the '94-98 units all have this, but the SVO unit does not have this feature. You will lose the low fluid sensor if you use the SVO unit. This will not cause the dash light to stay on, just permanently off. For the E-Brake light on the dash to come on with the E-Brake, you need to make a jumper in the connection you just removed. Connect pins 2-3 (the 2 purple wires, not the black ground). Be sure to label the connection to know what it is for in the future. For the '93 Cobra and '94-98 units, it is a direct plug in.
Which Master Cylinder?:

87-93s: The 87+ mustangs all use metric threads on the master cylinders. They are 3 port units, thus you must convert to a 2 port setup to use any upgraded master cylinder.

3-2 Port Conversion Products
The SVO unit was a very popular swap until the '94-98 units came readily available. It is very inexpensive at $15 rebuilt, has a large bore, but requires adapting to SAE threads and you lose your low fluid sensor. Do NOT use this unit unless you have the SVO front 73mm brakes and rear SVO brakes
The best all around unit is the '93 Cobra with the 1" bore, but it is more rare and it cost more. Its bore size is about ideal for most any brake setup out there presently. This is the unit I would recommend from most all brake swaps!
The '94-98 V6/GT MCs would be good compromise for most everything with the addition of a 94+ V6 brake booster or use of the larger 99+ GT/V6 PBR front calipers. You can find these for about $25 used at yards with the reservoir included.
If you are planning on running the Cobra or Brembo brakes, then I would suggest the '93 Cobra or '94-95 Cobra 15/16" MC with the stock booster. This will give you a pedal that is not to hard.
The last consideration is the cam in the engine. I make my recommendations off a stock 87-95 cam. If you are running a larger cam with less vacuum at idle, either drop a size in the master cylinder bore or set up to the larger 94-95 brake boosters to compensate. If the pedal is to firm after the master cylinder swap, then swap in the larger 94+ V6 vaccum brake boosters. Any of the 94-95s and 94+ V6 units will work. They are all larger than the stock 87-93 V8 unit, thus will give you more assist. I would not suggest trying to find the largest Sn95 booster available since they are all larger than the stock unit you are replacing - but finding the most cost effective unit.

79-86s: Since you already have a 2 port SAE threaded MC, you can swap one from a different car. The '85 Lincoln Towncar with a 1" bore is about the best unit for most all brake upgrades.

Which Master Cylinder to use on fox3 ('87-93) cars with SN95 brake parts:
Well since you are using the Sn95 parts, you should use a SN95 master cylinder as they are designed together from the factory. Either the 1" 93 Cobra unit or the '94-98 V6 master cylinder will bolt directly into the PV to MC fittings that you have! You just need to convert the stock 3 port setup to a 2 port one . You can do this with fittings under the proportioning valve to keep things clean! The low fluid sensor is even a direct plug in!

If you use the '94-95 Cobra master cylinder for a softer pedal feel, you will need to get 2 fittings to swap the lines on the master cylinder. The cobra has fittings that are the opposite of the v6/GTs so they did not get mixed up on the assembly line.

Now you need to convert the stock 3 port MC to the newer 2 port MC design. You can either purchase a 93 Cobra combination valve from Ford for about $60, or use a 3-2 port conversion kit. The 3-2 kits is a T fitting that screws into the bottom of the PV and has an adapter for the 3rd port! It will work with the the '94-95 GT/V6, '94-98 V6 MC, the '99 V6 units, the '94-95 Cobra, and '93 Cobra MCs! No Cut, No Flare! 3-2 Port Conversion Products
The other option is to use the parts from a '94-present NON-ABS mustang or '79-86 Mustang. They have a large fitting and special nut that will screw into the back of the stock combination valve. You will have to cut your stock 3rd port line and double flare the brake line there. Be sure to not remove any of the shuttle valve parts in the rear of the combination valve if you go this route.
Master Cylinder Notes:
The '96 and newer V8 Mustangs use a Hydroboosted master cylinder. The mounting flanges are vertical vs. the horizontal flanges required on the vacuum boosted units. Thus they are not compatible with vacuum boosters in the earlier mustangs!

The stock proportioning valve will need to be modified if you go to rear disc or to install an adjustable proportioning valve. You will need the FMS part: M-2450-A and an adjustable proportioning valve to complete the modification. The stock PV is housed in the front part of the combination block. This block is under the master cylinder and houses the PV and shuttle valve or pressure differential valve.

Why do you need to modify the valve? Because it is designed for the specific car and brakes that come with it off the assembly line. So if you change to different size brakes, you will need to change the front to rear bias via the proportioning valve. If you do not, then you will not get the most braking capability out of the car. Worst case scenario, you have too much rear bias and the car spins around when the brakes are applied. Not good on a rainy night!

If you have a Sn95 PV, why not use that? For the same reason you are not using your stock PV. It is not setup correctly for the amount of bias you need. The Sn95 valves are setup for the Sn95 car's weight, braking system and bias requirements. If you do find a 94+ car without ABS or 79-86 , you will notice that they are setup for a 2 port master cylinder. You can swap the end nuts on the combination valve and use this fitting as long as you cut and flare the nut from the donor car to make a factory like 3-2 conversion! You will not find those size of brake nuts at any parts store! Alternatively, you can remove the front internals and cap and transfer that to the fox3 combination valve and that will work to the Sn95 bias specs. This may not be the best bias for a fox3 car, but will work. The solution is to defeat the stock PV by gutting the unit and running an adjustable valve.

Okay, so how do you "gut" this proportioning valve? You use a 13/16 wrench and take the front cap off of it. Be careful as once it is loosened, the spring will shoot it out! Then remove the spring, the spring seat and rod. You may need some needle nose pliers to remove the rod from the valve. Do NOT remove the rear spring and rod from the rear of the valve. If you do modify the rear of the valve to work like the FMS M2300K kit or tap the rear for the 3rd port, be sure to install the rod and spring back in there!

Once you are done modifying the stock valve, you need to install an adjustable unit. There are two kinds of adjustable units: **** style and lever style. The lever style is more designed for an in-car application so that you can adjust the bias as the tires and brakes wear down in a race. You want the **** style. To install it, remove the coupler along the passenger side firewall and replace that with the valve. [pic]

When you bleed the brakes, adjust the valve all the way in for the maximum rear pressure. Once done, adjust the valve all the way out, and then in 4 full turns for your initial setting. Adjust in 1 turn increments from there and then half turn increments to fine tune. You will feel the braking and the pedal differ as the bias is changed.

Once you have the larger master cylinder on your Mustang, you may find that it takes more pressure on the pedal to lock up the brakes then you would like. First, check all the vacuum lines for dry rot, cracks or holes. Replace all hoses that look skeptical. This will restore the vacuum for the booster to work properly.
If that still does not help, then you can consider two options. The first being to change to a smaller master cylinder. The second it to upgrade the brake booster. Any of the 94-95s and 94+ V6 units will work. They are all larger than the stock 87-93 V8 unit, thus will give you more assist. I would not suggest trying to find the largest Sn95 booster out there as any are larger than the stock unit you are replacing. If you have heard about the Cobra brake booster, the same unit in the Ford M2300K brake kit (same as 1994-1998 Mustang Cobra and 1993 & 1995 Cobra R), you probably have heard horror stories about installing the unit. You do NOT need to beat the strut tower to install this unit for most all 87-93 installations. Remove the old unit and the lower hole in the firewall you need to elongate down about 1". This will allow the unit to slide right in!
Cost $100-200 depending on if it is reman or new. You may be able to find one from a person selling it from their M2300K kit for cheaper.