The rubber boot is not "necessary" per sé, but does keep a little extra junk out of there for a potentially longer seal life (especially with power brakes), and to keep brake fluid from entering the cabin when the seal does finally leak (only on manual brakes). Not a deal-breaker, but nice to have.
A bonus, if you want to look at it that way, is that you'll know right away whenever the seal does leak!
Some things that cause an initially spongy pedal might be, first and foremost, some additional air in the system somewhere. Second might be the rod length. Third might be a caliper that is pulling too far off(wtf!%)) the rotor. And old soft rubber hoses can do it too. A worn out master cylinder can do it too, but since this one is new, we'll have to assume it's ok until the very last thing. Not unheard of these days for new parts to be defective, but we'll hold out hope that this is not true in your case.
Rear brakes that are slightly out of adjustment can contribute greatly as well. To test that last theory, push the parking brake pedal part of the way down. Now drive it and see how the brakes feel.
If they firm up nicely with the parking brake applied, you need to tighten the rear shoes slightly.
The rod length shouldn't be an issue, since you're using stock to replace stock. However, it wouldn't be the first time there has been a variation. Didn't the new master come with a rod already in place? I know some don't, but I thought most did still. Either way, that's the least likely to be the issue. Just not impossible, so don't ignore it if nothing else works.
Air is just more bleeding to make sure. Bleeders on the calipers must be in the vertical, or close to vertical position to work. If yours are at a more acute angle, you might have to fiddle with it some more.
If any of the soft lines are old and worn, they might be allowing some air inside, or flexing enough to make the pedal spongy. This usually doesn't fix itself on the second pump however. Inspect them anyway, if you haven't already.
Make sure your bleeder hose is not allowing a little air back in every time you bleed. That's about all I can think of to do regarding air. Other than bench-bleeding the new master (did you do that?), you're pretty much limited to re-bleeding the wheel cylinders and calipers.
If it turns out that, for some reason, your Ford calipers are pulling back too far, for whatever reason, you might have to install a 2 lb. rated residual pressure check valve. Yeah, I know, you went to all the trouble of removing the old one in the master. But that was more like a 10 lb unit, and too much for a disc setup. But disc brakes can need some little residual pressure in the lines sometimes too.
I don't know anyone here, nor have I heard of anyone anywhere needing to install one on a Bronco. Hot Rods? Where the master is low? Yes. But Broncos? Might have some out there, but I haven't run across one yet.
You may be the first. But we'll hope for the other things instead. Like a little residual air, or rear brakes needing some tweaking.
Good luck.
Paul
