I also have a 5.4L vibration problem. I've been to the dealership twice and been told it was normal. Yeah, right. I have a 99 4X4 F-150, and it does it only when stopped and in drive with my foot on the brake.

 

It looks like this post is quite old, but I have the same problem.
I have a 99 F150 4X4 5.4L and I have had this into the dealer quite a few times. First they told me it was a problem with the Octane I was using. then they told me it was a "Harmonics Issue" and there was nothing they could do. Then they finally told me it was just like all the other F150's on the lot, and I should not worry about it.

Does anybody have a clue?

 

I have a 1998 F-150 X-cab with a 5.4 and it always had a slight vibration in it since day 1 I bought it . The tech's say sometimes it's the computer trying to compensate for the different air to fuel ratios at different temperatures. I say that's bull!!!!. My uncle who has been a Ford mechanic for about 20 plus years keeps telling me I'm putting to much oil in the motor and that's what's causing the problem. the owners manual says 6 qts. but it doesn't registers full on my stick. I usually put 7 qts. in it but when I put 6qts. the vibration went away at idle.

 

I have about 60,000 miles on my 99 5.4 4X4 and have had no problems as of the present with the vibration getting worse or damaging anything. I use Mobil 1 and I just noticed it started actually burning oil the past 2 oil changes. It still runs strong and smooth.

I also souped up a 2000 Expedition for a customer and noticed that after the mods (the same ones as on my truck), I noticed a slight vibration that wasn't present before. My guess (and that's all it is) is that the computer is somehow affected slightly with all of the different parameters that have changed.

Mods: Borla Cat-Back
Gibson Headers
K&N FIPK
Power Tower TB Spacer
Superchips Microtuner

These mods also on a V10 Super Duty make it scream! Much more noticeable than on my F-150.