Thanks for the question.
Is there any fault codes in the computer?
The o2 sensors would be the last thing to look at unless you had a code in the computer for it.
Has the fuel pressure been checked?
Well, it sure does sound like the it might be in the fuel system.
I would try replacing the fuel filter first if it hasn't been done for a while. If it still does it, I would get the fuel presssure checked, because as you know these v-10 suck a lot of gas, and the fuel pump needs to be at its best.
Also, you might want to try to unplug the MAF or mass air flow sensor and drive it to see if it is any better. If it does, you can try to clean the MAF sensor wire where the air goes through.
Thanks for checking that for me.
I did find the TSB you're talking about, but your concern is well after it is warmed up. This is what the TSB says:
Some F250-F550 Super Duty and Excursion vehicles equipped with a 5.4L or 6.8L engine, and some E350/450 vehicles equipped with a 6.8L engine may exhibit a rough idle and/or hesitation when accelerating. This may occur intermittently within the first 2-3 minutes after start when engine is not warmed up (ie., conditions other than hot restart). The condition is more likely to occur at ambient temperatures of approximately 60° F (16° C) and higher, and may be aggravated by an unmetered air leak or exhaust leak.
This is saying during the first periods of warmup. So I don't think this is your concern.
You may want to unplug the vacuum line going to the egr valve and see if this makes a difference. I have has a few of these egr valves cause some headaches in the past before.
Let me know how that works.