I just took delivery of my 2006 FEH, dumping the old minivan, now I am ALL hybrid (prius and FEH)....

To answer your question, I saw a "trip tunes" option in the FEH catalog (freely downloadable from Ford's website). Unfortunately even though a part number was listed, the dealer had ABSOLUTELY no idea what I was talking about.
Theoretically it is supposed to add a glove compartment minijack input to your audio system.

I couldnt wait, so I ordered the PIE X3 brain and harness (I have the Navi radio and cd changer under the seat). It comes with 3 auxillary ports and a cool lighted remote switch. It installed in literally 5 minutes and I have iPod input directly into the headunit via the cd changer harness...No FM modulation stuff.....works very well and I have 2 more inputs for XM, Sirius, etc.

look into it at logjam electronics...they shipped it same day for no extra cost...total price delivered...$97.00...sadly, no direct control of your ipod, however I ordered dlo's transpod which has a lineout minijack and it sits very nicely in the cigarette lighter 12V outlet at the base of the dash...Easy to read, easy to get to, and removable.