It could be a clutch master cylinder, but one other thing to check is the linkage itself. I'm not sure how a Jeep's linkage is set up, but I have had problems with a couple Fords over the years of slop getting into the clutch linkage. There's pins, bushings, etc that can wear causing slop. A fraction of an inch of slop can cause what you are describing. It could also be that the clutch cylinder is loose on the firewall and physically moving in and out when you push the clutch in.
There's also usually a splined arm that operates the linkage. It's extremely rare, but one could slip and cause you to not be able to push the arm far enough to drive the piston in.