One problem related to clutch pedal/linkage has been reported for the 2009 Jeep Wrangler. The most recently reported issues are listed below.
2009 Jeep Wrangler x 2 door manual transmission transmission first gear pops out of gear during acceleration. Shift to first, let off of clutch with or without throttle applied and the transmission will kick out of first gear, leaving the vehicle and occupants in neutral in an intersection, or on train tracks from a stop, forcing quick clutch pedal application and shifting into first again, with the problem most often recurring. This happens every time the vehicle is driven. This does not happen in 3rd of 5th gear. Dealer did a diagnosis paid for by owner, and determined it was the 1/2 gear and synchro gears. Chrysler has a technical service bulletin that I was ineligible. Vehicle had 20k miles when purchased, 25000 when diagnosed, now at 46,000 miles, with an even more often occurrence.