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The first one is a EGR code. Do you have an EGR delete?
The other is a turbo underboost code. Could be a few things, most likely would be vains sticking in the turbo. Also could have just been a one time type of deal. Try clearing the code and see if it comes back. Are you having running problems, or just checking for codes and finding those two?
Well the EGR Delete would be the reasoning for the P0401.
What year model truck are you talking about here? Any other mods, other than the EGR delete? What about maintance? when was the last time the oil was changed, and what wieght oil was it? Any smoke when it is running ruff? Those are a few things we will need to know to get started trying to help you.
Might be a case of injector sticktion. What about your FICM issue you had awhile back? Did you get that fixed? Also the ICP code you were getting, is that fixed now? You might try unpluging the ICP while the truck is running ruff, and see if it clears up the problem. Does it idle ruff? or is it just ruff when you try to drive it cold? After a few miles of driving does it start to run better?
Have you ever tryed to unplug the ICP to see if that clears it? Are those the only two codes you are getting? What are you using to get the codes? Is it just the edge tunner? If that's the case I would recomend trying to get somthing like Autoenginuity with the Ford enhancement package. That will help you narrow down the problem you are having. I really can't think of much else to do to figure this out without having something that will do more test. You don't by chance have, or no someone that has, a spare FICM do you? If you can get your hands on one for testing, try to switch them out. FICM can still be bad even if it has good voltage.