One problem related to clutch pedal/linkage has been reported for the 2006 Nissan Xterra. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Nissan Xterra based on all problems reported for the 2006 Xterra.
Vehicle slowed down on the freeway, took almost full power to maintain 20 mph speed. Burning smell in cabin accompanied the loss of power. Vehicle towed to original dealer. After a day, he stated it was the manual clutch assembly. Vehicle has 27661 original miles, this is the second manual transmission/clutch failure since I bought the vehicle new in 2007. First failure occurred after only 7954 miles. First time, the dealer said he didn't have to cover repair under warranty ( "wear" parts), but did it anyway because they believed there were no "driver" issues, ie. , part failure, not driver mis-use. As an aside, my wife and I have been driving manual transmission vehicles for 40 years apiece, and never had this problem. This time, two months out of warranty, dealer claimed Nissan would not cover the repair. $2100 later, I drove off the lot with a clutch pedal very much softer than when it was new. I test drove it with the repairing mechanic, he said he had adjusted the pedal play to factory spec, and the clutches should last 60-70000 miles (seems low to me-manual transmissions are usually bullet-proof with other manufactures ). Mechanic replaced flywheel, clutch disc, cover assembly, bearing release and first shaft bushing. Awaiting response to appeal for cost coverage from Nissan. Multiple clutch failures reported on the internet ( edmunds. Com, facebook ) for same year/make. Believe a poor design/parts manufacturer is the cause of these failures, Nissan needs to recall and repair these vehicles.