Last fall my clutch throwout bearing disintegrated while I was on my way to run the Rubicon Trail.
I limped to Elko, NV and had an independent shop replace it for me. It ran $800 total, including the new clutch kit, a new flywheel, a new slave cylinder (which he suggested on general principle) and labor. What I learned from this:
#1: do NOT
have the flywheel turned! This tech would have turned mine, but I ended up having him install a new one just to save time (he would have needed to farm it out). After returning home, I learned that Jeep specifically says the flywheel has a special conical finish which should not be turned--only clean it off with emery cloth if it needs it.
#2: bleeding the clutch lines is a royal pain in the butt to do properly. These guys tried (since they replaced the slave cylinder) but failed, and I didn't know it until I began to drive home--air in the system soon rendered my clutch pedal completely useless, and I had to drive 250 miles home shifting clutchlessly (which is no fun in the mountains of I-80). Because of this, do NOT
let your mechanic talk you into breaking the seal of your hydraulic system unless you have a component which has actually failed.
#3: inspect the entire Jeep carefully before leaving the shop--this includes crawling under your Jeep and checking that the trans mount's four nuts are properly reattached. My guy's air tool broke off two of the mount studs (which is very easy to do), so they just gave it to me like that and off I went in ignorance until I crawled underneath the Jeep three months later and happened to discover it.
Once my home mechanic was finally able to bleed all the air out of the lines (which took two efforts), it finally all works beautifully now.