for question 1.) is it fucked up in iTunes or your iPod? if it's iTunes... delete all your songs.. (just from the library don't delete them from your computer obviously) then add them back in... I used to have an issue because I keep my music on an external drive... that i'd read every song twice... then I'd go and delete the ones I thought were dups only to find out it was pointed at the same file as the one I wanted to keep.
question 2) naw you have all the options I know of listed... I'd go with the aftermarket stereo... something with an headphone jack so you still use the ipod to choose the songs... I've used the FM modulators and an Alpine changer plug and though the alpine plug sounds FAR better... it's a pain in the ASS to use the iPod through the alpine head unit... (if I had a motorized screen one it'd be a diffrent story) so I used the FM modulator alot
question 3)
This what your talking about?
question 4) I personally went with the Shure e2c noise eliminating headphones... they fucking rawked... but they're not cheap... $100-110... I could put them in and turn them up 1/4 and couldn't hear anyone around me in a normal area... 1/2 volume would kill any sound short of a jet... and full volume I couldn't hear ANYTHING... even a fuck'n jet.. (I walked by one in Kuwait and seriously couldn't hear it)