I've never run into this on a Ford before, but this is very common on GM front-wheel-drive cars so I'll share my answer about those cars, but first let me point out a couple of things. First of all, you should never push the brake pedal all the way to the floor. In this case you can get away with it because you have a new master cylinder. Once they get to be about a year old, crud and corrosion build up in the lower halves of the bores the pistons ride in because they don't normally travel that far. When the pistons do go that far, as in when being surprised by a leak while driving, or when pedal-bleeding with a helper, you run the lip seals over that corrosion and can rip them. The common result is a slowly sinking brake pedal and the need to replace the master cylinder.
Second, you didn't mention this but for the benefit of anyone else researching this problem, you have to bench-bleed the new master cylinder before installing it on the car, otherwise you'll waste a lot of time and brake fluid getting the job done.
As for that GM problem, almost all front-wheel-drive cars have a "split-diagonal" hydraulic system. Instead of the front brakes on one system and the rear on another as was done in the past, that puts the right rear and left front on the same circuit. There is a valve in GM master cylinders that trips when there is unequal pressures in the two systems, and that valve blocks fluid flow to two wheels. You will create unequal pressures when you pump the brake pedal and open one bleeder screw. The only way I have ever found to reset that valve is to open one of the bleeder screws that isn't flowing any fluid, then give it a quick, short burst of compressed air, then just let it gravity-bleed.
Once all four wheels have gravity-bled, stroke the brake pedal slowly a few times, (never more than half way to the floor), then open each bleeder once more to remove any remaining bubbles that washed into the wheel cylinders or calipers.
Monday, January 21st, 2013 AT 2:48 AM