Exhaust leaks a good start, a small one will sound like a tick, as for the rest, im not up on the 3v 5.4 and never had any of these issues on either of my 2v 5.4s, just the infamous exhaust leak and coils/plugs. I know the 04 ups have the same exhaust leak issue. I know chris' roommates 06 has a pretty bad leak.
My 03 had a slight exhaust tick and it sounded like a lifter knock and everything else that was described. Hopes its as simple as that.
possibly, also on my 04 with the 4.6 2v had a exhaust leak around my cats. Tighten up the bolts and that made the engine very quiet.
I wouldnt **** with the manifold studs on these motors. Their ****ing garbage. Just when the time comes to put headers on buy some pb buster and grade 8 header bolts from ford racing. So **** doesnt break off in the head.