I know of more that haven't had issues (and are worked hard) than that do have issues. Some even have pretty decent tunes. It has a bad rap because the percentage of issues was much higher than average, but i bet that percentage is still much lower than perceived. Still, personally I would bulletproof cause I don't like bad surprises.
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I agree, they are MANY 6.0's out there that have not hand any problems. Mine is one of them. But, I believe there are several contributing factory of why mine, and many others have not had issues....
Mine (an 03) was bought new by an older couple. It was their tow vehicle. It had ~65,000 miles on it when I bought it 2007. I have all the paperwork from the couple of repairs from the original owner. They had to have the Stereo repaired, and had a couple of coolant leaks fixed. (Not EGR related) Also, in the owners manual, the recommended service schedule, has all the miles when each service interval was performed. EVERYTHING was serviced when it should have been, according to the book.
When I bought it, it had a set of tires put on it before it left the dealer. (This was going to be my "family car" and the tires did not fit that status... they were the factory BFG's with 65,000+ miles). It also had a noise in the front end that was "fixed". The dealer said it was ball joints, and replaced them. Actually the noise is the sway bar end links that attach to the frame behind the front axle. I actually still need to replace them.... it is an annoyance not a safety/drivieability issue.
In the 7.5 years that I've owned this truck, I've replaced:
Batteries/Alternator. Had an issues with the batteries, and they took out the alt. Then I had trouble with the replacements (rebuilds), now have a new replacement on it, and been good for several years.
All brake pads
Had to have the FICM repaired due to the battery/alternator issue. Low voltage will KILL the FICM
The Water Pump, coolant and serpentine belt. Pump started to rumble, so it was replaced.
Batteries, again. The 6.0 is ******* batteries, and most owners don't get over 3 years on a set.
The ICP Sensor (Thanks RON!!!!)
I've done an EGR Delete due to a coolant leak. The EGR Cooler was NOT LEAKING, the supply tube to the cooler was leaking into the valley and off the back of the engine. The proper fix was to remove the EGR Cooler to replace the supply tube, so I decided at this point, if it was coming off, it was not going back on.
There had NOT been a tuner on this truck...... and never will be. - I think this is a HUGE thing.....
At 143,000 miles, I still have the factory turbo, head gaskets, head bolts, and all the other parts it was put together with in 2003 at the Navistar plant here in Indianapolis.
It's had the oil changed at 5,000 miles with GOOD oil and Motorcraft Filter. The fuel filters at 10,000 mile with Motorcraft filters. I am now running Chevron DELO 5-W40 Full Synthetic oil.
I am extremely happy with this truck, and would buy another 6.0 without hesitation. It has been my daily driver of a 60 mile a day round trip and I get 15-17 in my mixed commute. I have seen as high as 21 on a long road trip.
Grab a 6.0, drive the wheels off it.... and if it does have an issue. Fix it, or if it can be made batter, do it and NEVER worry about it again. I have no plans on getting rid of this truck.... EVER!!!!!