Your fears with the horror stories can definetely be found on the 03-04 motors. The late 04 motors on up were far less prone to being hurt. The late 04 motors are different, pretty much you can tell with the location of the ICP sensor. Or looking at the manufacturing date of the motor. After August 05 Navistar(International) really tightened up there design and therefore made things a little better. With about 3500.00 on the 6.0 motor you cant beat it. If you purchase the model year 05 you pretty much get the same truck with the exception of the front grill and headlights. If you buy the 03-04 you can easily buy the grill and the Harley Davidson headlights. And if you really want the perfect truck, you want to build on a F250 Platform with the Alison Transmission and the Cummins 24V common rail, that would be the perfect truck in my eyes. But seriously with 3500.00 you can easily buy the items you need and an SCT with custom tunes and easily throw it on your rig and ride out. There are tons of guys that have done it. The problem is when some people throw the 150 CAN race tune on a stock motor and expect it to stomp ass, when all it is gonna do is fall on its face. You can do that but after it is all built and be safe about it.
Check this out, this is primarily what you would need to get pass the crap
6.0 Diesel Powerstroke EGR Delete Black Onyx Oil Cooler | eBay
Do the work yourself and badda-bing. Call Jody at Innovative Diesel and he can set you up with some custom tunes on an SCT Xcal and your ready to rock and can get you an economy tune as well, pull your FICM and Jody can also tune FICM's also for economy driving and runs the new flash on them. Supposedly people are saying running the economy tune and the FICM flash are yeilding about 20 mpg. I dont know the truth to that or if it is just propaganda.