I did not bench bleed the master by putting it on a bench, but here is
what I did.  I took a piece of hydraulic line and looped it around
from the hydraulic fitting in the master cylinder back into the
reservoir.  I disconnected the master cylinder plunger from the clutch
pedal and pumped it in and let it release until I didn't see any more
bubbles looping around into the reservoir.  I then quickly swapped the
piece of hydraulic line for the hydraulic line that goes to the
slave.

This didn't help much at all.  The pedal would get firm while bleeding
it, but soon after starting the engine the pedal would not engage
until close to the bottom of the stroke and the transmission could not
be put in gear.  I was skeptical on the clutch line because of issues
sealing it earlier, and I guess I like to continue to sink money into
this, so I replaced the clutch line.  I bled the system, but did not
re-bleed the master as above, and the clutch got real firm.

I bled it as follows: I had a friend pump the pedal a few times and
had her hold it to the floor.  I hooked a vacuum pump to the bleeder
valve and built up pressure. I then cracked the bleeder valve just
enough for fluid and air to escape.  I had a clear tube hooked up to
it and fed it into a small container with a couple inches of fluid in
it.  I did this 3-4 times until the air bubbles stopped developing.  I
made sure the master reservoir remained full.  I then repeated this a
couple more times without the vacuum pump and all seemed well (no
bubbles).

This seemed like it was going to work out.  I started the engine and
let it warm up, as it is now cold here again.  I went out and
depressed the clutch and worked it through the gears.  I did this
several times.  It was working so I thought all was good.  I went for
a drive and about 5 minutes into it the pedal went almost to the floor
before it engaged.  I could not get the tranny out of second gear
until I slowed and pumped the pedal several times.  It then would work
OK for a while then it would repeat.  I then noticed a pattern.  When
I replaced the clutch line I only connected one of the 2 bolts that
held it to the body (since I wanted to test the clutch pressure before
permanently bolting down since the bolts are tricky to get to),  When
driving I would sometimes here a loud rattle in the vicinity of the
clutch pedal area, but on the other side of the firewall.  This is
also the area where the rubber hose turns to metal on the clutch line,
right before bending under the vehicle.  The line is slightly
different than the original, but not significantly different.  I
believe the metal of the hose was rattling against the body pretty
rapidly, sounding like a bad vibration.  At this time if I tried to
shift the tranny, the clutch would not have much pressure at all.  I
observed this pattern continue as I limped the jeep home.  Rattling =
no pressure.  I had issues with maintaining pressure the whole way
home. What is weird is that it seemed like it was better when shifting
to third, but I couldn't observe a pattern there because I was scared
of being stuck in third, so it might have been coincidental that it
seemed good the couple of times I tried it.  At least in 2nd I could
cheat up to stop signs and lights.

When I got home I parked the jeep and went inside the house to
wallow.  I then came out a few minutes later and pressed the clutch
pedal.  It was solid as I pressed it.  Just like it was when I bled
it.  Not after pumping either.  On the first couple of strokes.

Anybody have any ideas?  I feel I replaced the various clutch parts to
spec.  It seemed rather straight forward.  I don't know what to do at
this point.