2005 X, not the 4.4 but the 3.0d,
points 1 and 2 I have been lucky enough not to experience yet.
point 3, yep I am with you, was told by the dealer it was normal

my is more the case of a bass rattle i think, but it seems to happen at quite low volumes. i have contemplated asking for the door panels to be taken off and everything checked to be secure behind.
changing the DSP settings to the article UCrewX5 pointed out to me did help, but didnt solve the problem
reading other posts i get the general feeling that people are not over the moon with the DSP stock stereo. definately something I will upgrade starting with the SUB at some point.