You may have the drum brake master cyl. which has equal size reservoirs. The disc/drum brake M/C has one reservoir that is larger than the other. The internal valving is different.
Another thing to look for is a proportioning valve. (not the distribution valve where all of the lines merge) The proportioning valve will be plumbed inline with the rear brake line only. If the rear brake line going from the dist. valve to the rear of the car doesn't have anything but brake line going to the brakes, it's missing. You will need to install one. The OE proportioning valve looks like a small cylinder, mounted where the rear brake hose connects above the rear axle housing. You must have this valve with a disc/drum brake system.
The proportioning valve controls the amount of braking force to the rear brakes, which should be less than the front brakes. You can loose control of the car if the rear brakes apply with greater force than the front. These valves are available in adjustable form and are just plumbed into the rear brake line.(Usually just after the dist. valve, under the hood on the driver's side inner fender) I've found them to be more reasonably priced than the preset OE type.
The manual brake pedal is different than the power brake pedal. The manual pedal's M/C pushrod mounting pin is located higher to the pedal's pivot point than the power brake pedal. If the correct pedal is installed, the M/C or booster pushrod will run almost straight across. If the power brake pedal was installed to the M/C without the booster the pushrod would be sitting too high and would be pointing in a down position toward the pedal. The correct pedal has the pushrod sitting in a straight horizontal position. All 68 Mustangs with factory disc brakes were power. I personally have good brakes with a manual disc/drum Granada set up on my 67. The Granada disc brakes are very close to the 68s design and you could go with a manual set up if you desired. | 
