I really liked my 03 F-350 6.0L Super Duty too. It pulled well in higher RPM's but was a gutless pig in low RPM's which was really apparent with mine because it was a 6 speed manual.
I did spend considerable money "bulletproofing" it which included EGR delete, coolant filter, regulated fuel return system, turbo cleaning, and upgraded turbo oil drain tube. The EGR delete made the turbo spool considerably quicker and I didn't have to keep dealing with surging due to sooted up EGR valve which I had to before.
Although I loved the truck some of the horror stories were constantly in the back of my head, and I was getting more nervous while towing our trailer far from home. The truck was approaching 12 years old and had 110,000 miles. It had a constant oil drip from the bedplate and it was stumbling a bit when started cold which made me think I had an injector or two getting weak. Plus it was a Supercab and we needed a bigger cab for our 4 year old son who is growing like a weed.
I tried selling the truck privately but the reputation of the 6.0L shied all but the lowballers away. I then was shopping around for a newer truck and was offered $8-10k on trade for it because dealers really did not want it and even told me outright that they would likely auction it because of the engine. I got very lucky and found the left over 2013 truck in my signature that had a good sale price on it and I was pleasantly surprised to get $16k on trade for the Ford.
I do believe that a 6.0L truck can be made into a reasonably reliable truck with the proper modifications, and I also believe that Ford had the nicest truck in the early 2000's with the Super Duty. Just be sure to buy at the proper price because they are very tough to sell for a decent buck at the end of the day. For comparison, equivalent 7.3L Super Dutys, GM, and Dodges from the same era were selling for $10-15k more in this area.