Join Date: Nov 2009
Location: The southern armpit of California
From what you describe I would guess that the clutch plate isn't fully disengaging from the flywheel.
"Bleeding" refers to getting any air out of the clutch hydraulic line. This is done by opening the bleed valve at the slave cylinder and having a helper pumping the clutch a few times to force the fluid and bubbles out of the line, then quickly closing the valve again (while the clutch is depressed) so that air does not get sucked back into the line. Repeat until the clutch pressure and shifting behavior is back to normal. You also need to keep an eye on the fluid level in the reservoir and keep it topped off with new fluid as necessary (it drops really quick), or else you just end up with more air in the line.
The first step though in dealing with clutch/shifting problems is to check the fluid level. For the YJ, the clutch reservoir is located on the firewall, driver side, just under the grill support rod. There should be level indicators on the outside of the reservoir, but if you really want to be sure you'll need to remove the cap. In order to remove the cap you'll need to remove the grill support rod.
Next step is to perform a bleed.
If bleeding doesn't solve the problem with shifting, then there is likely a mechanical failure of the master cylinder, slave cylinder, clutch plate assembly or a problem with the sychronizer gears in the transmission.
I had a similar problem to what you've described, although with a transmission on a Ford Ranger. In my case though it would start to act up only after the transmission warmed up. Turned out to be a problem with the clutch plate assembly.