If you run statistics on the proportion of modded trucks that have some kind of engine or drivetrain problem and compare that to what stockers display, I am certain (I don't have the numbers, but I'll bet a significant sum) you will find a significantly higher number of modded trucks report problems.
So, the mods somehow are likely to blame for a lot of problems. Let's be honest, adding power is the easiest way to add stress, and those components that can't handle the added stress will begin to fail.
Now, one of the mods that can do this damage most easily are the chips or tuners. It is very tempting to download a program and tap into an extra 100HP, isn't it? But with the desire to add power should come an appreciation for the ramifactions of that power. Besides making your truck bark the tires and all that other stuff, it will add stress to the tranny, to the heads, and other areas (like the number of EGR failures modded trucks have.....it's no coincidence that these richer tunes, which generate a lot more soot under certain conditions, happen to be in trucks that have EGR problems). Another factor is, as good as the engineers and techs are who develop the tuner software, how do they know that their changes don't have any other trickle-down effects? I don't know of any, but I often wonder if there are some built-in Ford programs that use info from the power management algorithm to make decisions on other systems that ultimately get fubared as a result of the tuner modifications. That is, the tuners don't replace the entire computer software system; rather it is just a subroutine-type insertion. For chips, the questions are similar. The bottom line is these tuners and chips increase system stress, and to really use the extra power, reliably, over a long period of time, the user must also address the various weakneses thus created.
As to fault, I don't think it is either the tuners' fault or Ford's. Ford is only culpable for things that happen on stock trucks. The application of extra power totally relieves Ford of any responsibility if anything in the engine/drivetrain fails UNLESS it also happens to be something that has a noted problem in stockers. I think the lion's share of responsibility for damage done after adding power lies with the user.
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We all have to have half a brain before deciding to add the power.....realize it is likely to damage a few things.....beef some things up before they fail if you can....but be prepared, because it is more likely than not that you will encounter a problem.
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I do think, though, that the companies that provide power upgrades should proactively educate their customers on the potential risks (I'm sure Banks runs their whole business model around this concept), and how to use their technology with minimal risk. I would say a tuner company is culpable if they sell their technologies with the disclaimer that it will not cause any harm.....and you'd have to be pretty stupid to believe them too.....