Ok, so I have tried some things, I will list them first.

Disconnect battery + and - for 20 mins.
Check air filter.
Clean MAF.
Check PCV tube to intake.
Removed intake and intake tube and check for anything inside it, or damage.

The only thing left I have not tried is the factory intake that came with the truck.
I have a factory on it, but its off another truck and I wanted to see what it would do with a gotts mod and the baffles removed from the tube.

Please spare me the "ur stupid" comments, as I plan on trying the orginal intake on it tomorrow.

The fuel filter was changed about 15K ago.
I switched from 93 to 87 about 10 tanks ago. I did try a 1/2 tank of 87 and added 1/2 tank of 93 and it seemed to lessen the problem or it went away completely.
I was thinking that the 87 may have some water in it, might try a different gas station.

The truck runs fine as long as you don't go past 3,000 rpm, or more then 1/2 throttle.
Anything higher than 3,000 RPM and 1/2 throttle an the truck cuts in and out around 3,500-4,000 then picks right back up and runs great.


Its just like a dead miss or the fuel gets shut off for a second and then right back to normal.

Any suggestions, or things to look for?
I have a 500 mile round trip coming up in three days, so I would like to get this sorted out.

 

I have an 06, mine started doing the same thing. I changed coils didn't fix, so I took the plunge and changed plugs, problem solved. I am in Bardstown KY if you need any help.

 

Well, I am going to try a fuel filter first, I hope its not the plugs but if it is I am fairly sure I can get them changed in a day.

Dad has the tool for removing broken plugs, hes done a few I think.

Thanks for the suggestion.

Edit.

Looking at over $100 for plugs, guess it has to come out of the vacation money.

 

I have done 7 sets of them now. You can get the motorcraft plug at advanced for $8 a piece, but the champions are still $19.99. It isnt hard just time consuming. Last set I did had 128000 on them and broke all 8.

 

I called around and for a 2006 flex fuel 5.4 all I could find at advance and Auto zone where $12.99 each in auto light and motor crafts are the dealer for $22.95 each.

No thanks, maybe if the $8 each ones would work, but no way can I afford to cut $160 for plugs right now.

 

Yeah last set a bought from Advanced was less than $70 for motorcrafts.

 

I would bet alot of money on it being the plugs. It sounds like exactly what mine was doing and after the plug change it is all good.

The plug change is very doable in a day if you have the tools. Mine has 95000 on it and I broke 3 out of the eight.

 

Flex fuel takes the same SP-507 or SP-515 that the regular 5.4 takes. Less than 10 bucks apiece from rockauto.com.