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On the first gen explorers, it's usually the slave cylinder. They go bad, and make shifting difficult, making it hard to engage a gear. I've never seen a master cylinder go bad in a first gen, but they tend to do better when bled so there is very minimal air in the system.
Unfortunately, replacing the slave is a full-on drop-the-transmission job, same as replacing the clutch itself. Replacing the master is a relatively easy under the hood affair.
You've never tried to bleed the system after installing a new master, haha. What a PITA! I would have wrather dropped the tranny. (yes I've done that too. And that took me LESS time to do!) It's just such a horrible angle to bleed the master with.
Actually, I had to install a new master cylinder after the PLASTIC clutch pedal rod busted on the original one. The new master was a funky design that was apparently to make it hard for air to stay in the system, and after install, bleeding it wasn't an issue, despite all I had read on needing to bench bleed them. Looking back, I should have just removed the broken plastic rod and stuck in the metal one from the new master...the clutch has never been the same since replacement, much harder to push.
The slave, however, continues to be a problem, going out every 50,000 or so, it's at it again, guess I'll spring for one from Ford this time and hope it lasts 100,000 like the original.