OK, here is one way towards perhaps gaining a better appreciation of the jams. You put ATMP on your iPod but with an altered order of tracks.
Just transfer the songs from CD1 as for the original first vinyl LP, deleting the bonus tracks. So far so good. Then CD2 is divided into four, following the four album sides from the second and third vinyl LPs, and rearranged, leaving the 6 original album sides in the following order: Side 1, Side 2, Side 3, Side 5, Side 4 & Side 6. This breaks up the unbroken group of jams at the end of CD2 which does not conform to the original album anyway, since it was necessary to turn the 3rd LP over to hear the last 2 jams.
So you go from the title track at the end of Side 3, to Side 5 starting with Its Johnny's Birthday then the jams Plug Me In & Out of the Blue, to I Dig Love at the start of Side 4. The end of Side 4 leads straight into the Side 6 jams I Remember Jeep & Thanks for the Pepperoni. The title track is my favourite song on the album and I Dig Love my least favourite, so I'm not really keen on how there is no break between them on CD2.
I find I am appreciating the unity of each of the last four vinyl sides. And its great to only hear a couple of jams at a time because it makes the differences between them more striking when you don't have to digest all four of them in quick succession.
If you've noticed that I've changed the Side 5 track order, its because I prefer Out of the Blue after Plug Me In rather than before Its Johnny's Birthday, which I think sounds great following the title track.