Brandon,
I am sorry to hear about the bad luck you are having with your truck. My only point was that Ford is going probably take a very hard look at your truck, seeing that you have done modifications to the intake, exhaust, and the suspected use of a tuner such as the Edge. Whether or not your truck was running poorly before the mods wouldn't matter in their opinion. It would be the condition of the truck as it stands NOW.
You live in Wyoming, so I gather the Ford dealerships are few and far between. Do you feel comfortable with the service department at your dealership? Do you feel your diesel technician is competent? Some of the problems that these engines have are due to misdiagnosis by less than competent technicians. These engines had their problems earlier in their production cycle, but there have been several design changes and improvements that have addressed issues of reliability.
I can tell you are frustrated. You can rely on the help of everyone in this forum, as I have found them to be some of the best people on the Internet, they know their stuff, and above all, are very friendly to newcomers. I don't think you have anything to worry about too much from the moderators. They will let you know with a PM if they do.
You've given us a bit more information as to what is wrong with your truck. Any more information might help. Again, it might be a simple, but agonizingly slow fix, especially if your dealer only has one technician and he's stacked up three deep with some of those OLDER 6.0 trucks!
We're all pulling for you for a successful resolution to your problem.