This is a very controversial subject when applied to the 6.0 Ford engine. I have considerable experience, good and bad, with this engine. Here are some of my opinions
on the tuning issue. I am sure there will be disagreement.
1. Do not do any upgrading of any components on the 6.0 powered truck before doing these three steps. Install a coolant filter. I recommend dieselsite or defuser brands. Install engine monitoring systems. The cost here is less than $200. For the majority of the monitoring needs, I recommend the Edge Insight Engine Monitor. It will cost around $400 complete. This is NOT a tuner, only a monitor. It will watch up to 24 parameters at once. Make sure you order the optional exhaust temperature probe. You need to monitor the engine oil temp/engine coolant differential. It is vital to your engines health. Iff you have more than 15 degrees difference in these temps, you are in the midst of an evolving oil cooler failure. However, in almost all instances the egr cooler lets go before the oil cooler. I have written here before about these issues. The Edge Insight will help you avoid a costly failure by warning you of its impending status. The third upgrade is a fuel pressure gauge,This is important for a stock truck, mandatory on a truck running performance enhancements. There is no way to monitor fuel pressure from the OBD port where the Edge Insight plugs in. This information, along with oil pressure, is not supported on the 6.0's computers. There are two routes to fuel pressure monitoring. Both are gauges, the difference is pricing. The economical route is using GloShift.com for your gauge setup, about $100. I went with ISSPRO EV2, Made in USA, for $200.
2. Do not use programmers from any manufacturer that advertises tune on the fly. Bullydog, Banks, Edge and others advertise these products. They have proven quite problematic with the 6.0. The 6.0 Ford/IH diesel was a leader in computerized engine and transmission technology when it was introduced. To truly tune this engine and transmission combo,the computers must be rebooted for the proper changes to take place. Think of it as having to reboot your Microsoft Windows computer after making any changes to make the changes work. Tune on the fly tuners are not really programmers. They work by digitally lying to youe truck computers to over fuel the engine, hence more power. This practice is hard on the engine and has proven to be very hard on the otherwise bullet proof 5r100 automatic transmission.
3. The absolute programmer of choice for the 6.0 is the SCT X3 programmer from SCT. This is a true programmer. All tuning changes require shutting the engine down, program while shut down and then a restart for programming changes to take effect. The engine and transmission computers are both programmed. If you watch the display, it first tells you it is programming the engine computer. when the engine is programmed, the display switches to telling you that the transmission is now being programmed. Although there are several respected 6.0 tuners writing custom tunes for this engine, Eric at Innovative Diesel is probably the most popular. When you order the SCT X3 programmer from Innovative, you will get three custom tunes of your choice. You will be asked what your truck has for modifications, stock head bolts etc and what do you want to accomplish with the programmer. I ordered their 60 hp street tune, their 120hp aggressive street tune and their heavy, above 10000#, towing tune. I was very happy with all 3 choices. I ended up running the 60 hp tune all the time except for when I was pulling the Big Horn. I ran the heavy tow when pulling the fiver. It is a sweet tune. You will see a big difference and get an exhaust brake for free. They tune the turbo to actually act as a brake. It works great. The 120 hp tune was way too much fun. A 8400# truck should not be that fast. I only ran it when I wanted to show off.
4. You can safely run a SCT X3 programmer on a healthy stock truck. The stock truck tunes have been designed to run at stock cylinder pressures. I must stress though, your truck needs to be healthy beforehand or potential problems will arrive on an accelerated schedule.
There is a lot more knowledge now on the real issues that have sullied the 6.0 reputation. Many of the reliability enhancements available have been the result of experiences only truly understood over the last two years or so. The head bolt/head gasket issue was originally believed to be a design flaw in the 4 bolts per cylinder block design. We now know that more failures are related to egr cooler/oil cooler failures and the subsequent cascading of bad things that happen when this occurs. There was also a huge problem with inexperienced technicians trying to use old knowledge to fix new problems. Unfortunately, this still goes on. I am sure some will disagree with me and they are entitled to their opinion. I will not argue with them here. Too much of that at RVnet.
Regards