03/04 have the old cylinder head design. I would stay away from them unless you owned it for a long time and you knew what kind of maintenance was done to it. 03's in particular have the old egr cooler, but if it's been deleted, probably not an issue.
The 5r110 that came in the trucks starting in '05 is worth the money. Way more stout than the 4r100 and really makes the truck drive nice. I wish I had one in the RV. Mac does and it makes a big difference in how the truck drives.
My 6.0 is puking white smoke, which based on a cylinder balance test and some other troubleshooting, is either an injector or the turbo is stuck. I'm going to clean the turbo this weekend and go from there. 6.0's like frequent oil changes. If you're not comfy with $80 every 3-5000 miles, you're asking for trouble with your HPOP and your injectors.
FICM's tend to destroy themselves because they're mounted to the engine. A FICM that puts out less than 45 volts will cause the injectors not to fire. There's a few places on the net that will reman your FICM so you don't have to spend the $800 on a new one, but it's still something to be concerned about if it's never been changed.
I've owned mine for 100k miles and had the FICM and HPOP replaced under warranty. The heads were off and on before I bought it with 29k miles. I'm not studded, the egr is still there (the valve is off) and I've been running a tune for 6 years. The white smoke issue is the first time it's let me down. 2 trips to moab, multiple trips to WF and Harlan and DD everytime it rains.
If you do your homework and make sure that the used one that you're getting is not someone else's headache, it's a truck that will last a long time. I wouldn't buy one without the ability to hook it up to diagnostics and check the coolant/oil temp delta, the FICM voltage and the ICP pressure. If those look good, it's probably a well taken care of truck. If they don't want to show you those things, I would walk away.
Oh, and out of the box with a computer program, I have a dyno slip for 384 hp/711 tq at the wheels. When they run, they run