x2 on not resurfacing the flywheel. Jeep officially suggests cleaning it up with some emery cloth; if it is too scored or damaged for that then replace it with a new one.
My advice learned through recent experience: for the love of God, do NOT crack open the hydraulic system and replace only the slave cylinder! If your slave seems to need replacement, do the smart thing: buy the pre-assembled and pre-bled master/slave assembly from Chrysler.
The TJ's hydraulic system is a complete, total, royal, colossal pain in the ass to try and bleed. When my clutch had to be replaced in Nevada last September, the tech talked me into installing a new slave cylinder. He spent lots of time bleeding it and it seemed good, but ~20 gear changes after I left their shop, air in the system suddenly caused my clutch pedal to become useless... and I had to drive home from Elko without a clutch... through rush hour traffic in Salt Lake and Utah counties. Back at my dealership, it took my tech two additional tries at bleeding the system (plus an entire bottle of brake fluid) before it was finally in proper working order.
Save time, prevent endless headaches and frustration--buy the pre-bled system.