Here's an update to this old thread on what has been happening with my Wrangler. I have experienced it all- the rattle in neutral, the squeaking in the transmission when the clutch pedal is released/depressed, the squeaky clutch pedal, and the slave that went out and my pedal went to the floor.
So I have had my throwout bearing replaced three times (all under warranty), and the clutch slave replaced (not in warranty), and the neutral rattle is gone. The other week, the pedal started creaking again. I'm thinking the slave is going to take a dump again, but the last repair was warrantied for a year, so if it does, I will be covered.
After multiple visits to the dealer I have also had the clutch fork replaced. The last time they went into the tranny they said the clutch looks great. I have resigned myself to the fact that the manual transmission in its stock form is terrible, and I am going to drive it until the clutch goes, then replace it with a good aftermarket setup. It's just very frustrating dealing with all these issues on a relatively new (under 46k miles) vehicle.
I love driving a manual, but all these issues have me wanting to jump to an auto.