I'd have to say that if your crank moves forward far enough when you depress the clutch pedal for the flywheel to hit the dust cover, your thrust bearings are gone. Do you idle with the tranny in gear and your foot on the clutch for more than a few seconds, such as when stopped at a light? That's the most common cause of thrust bearing wear. Depressing the clutch pedal on cold starts is a cause of wear as well.
You can drop the oil pan, loosen the main bearing caps, and replace the bearings 1 journal at a time. Afterward you'll need to check end play, which is simple and requires a dial indicator and prybar (a lead hammer comes in handy but isn't necessary.)
ETA did you forget to install a spacer between the crank and flywheel when you did the work? I haven't had a Jeep tranny out in forever so I can't remember if there was a spacer.
'90 YJ w/4.2l & 4.0l head, Weber carb, 5-speed, 4" RC lift, 33x10.5x15 BFG MT KM2s.