1995 Ford Explorer

A tip to bleeding that system is first take that little rubber cup out of the master cylinder resevoir, fill the resevoir up, have someone pump the pedal 4-5 times and hold it on the floor, open the bleeder to release air and fluid, release pedal, u may have to pull it up, repeat this 3-4 times. If this does not help, the next question would be did this problem start all of the sudden or has it gradually gotten worse? If it has been an ongoing problem that progressively got worse then I would suspect the blocking rings inside the transmission, if worn the trans. Would be hard to shift, and may come out of gear at times.

We have bled the system the way you have said, and yes the problem did get worse over time, we can powershift it, does that make a differance as far as something being wrong inside the trany?

The blocking rings are part of the synchronizers and slow the geartrain when shifting, if they are worn, shifting is going to be difficult any way you try to. To rule out the clutch system, I would have someone press the pedal while watching the slave cyl. Travel, you should have noticeable travel, if so then internal tranny problems are likely, if you have very little travel then I would suspect the master cyl, considering all other components have been changed.