Now I have to pump the clutch to get it in gear.

There is either a leak in the hydraulic clutch system. The system starts at the master cylinder which is a smaller version of your brake master cylinder. It is just to the right of it when facing the truck from the front. Check for leaks and look at the level of the fluid inside. Then it runs through a hose to a slave cylinder which actuates the clutch. Look for leaks here.
You may have air in the system and need to bleed it.
You can get a bottle and some clear hose that will fit snugly on the bleed screw, on top of the slave cylinder, to cath fluid that comes out as you bleed it. During this entire procedure make sure the level of fluid in the master cylinder stays above the low mark as letting it go down too far will pull air into the system. Get a high quality, preferably a flare wrench or six point box end, that fits the bleed screw and put it on so you will have room to loosen it. Put the hose on the screw and run the hose above the screw and down into the catch bottle. Have an assistant pump the clutch a few times and hold it. While the pedal is held down loosen the bleed screw and fluid will come out. Tighten it back and then your assistant can let the clutch pedal up off the floor. You might see air bubbles as this would be air in the lines. Repeat this procedure until there are no bubbles present in the hose.

CHECK YOUR CLUTCH MASTER CYLINDER FLUID LEVEL

SYSTEM MAY ALSO NEED BLEEDING

IF YOU NEED ASSISTANCE WITH THIS, LET US KNOW, RESPOND AT THIS POST

THE MASTER CYLINDER IS ON THE ENGINE SIDE OF THE FIREWALL, OPPOSITE OF THE CLUTCH PEDAL

LOOKS LIKE THIS---FILL CAP IS ON LEFT END

http://www.autozone.com/autozone/parts/Duralast-Clutch-Master-Cylinder/1994-Jeep-Wrangler-4WD/_/N-j0o86Z6o23x?counter=1&filterByKeyWord=CLUTCH+MASTER+CYLINDER&fromString=search&itemIdentifier=227053_0_0_

IF YOU HAVE OTHER QUESTIONS INCLUDE COMPLETE JEEP NOMENCLATURE AND ENGINE SIZE

I HAVE MORE EXPERIENCE WITH CJs

YOUR TURN

THE MEDIC

Check the clutch master cylinder fluid level and also the clutch servo/slave if its leaking if not bleed the system and see what happens-if it needs pumping to engage the clutch -might consider replacing th master cylinder for a start could be leaking internally