It's pretty clear from the inlay below that the brain in the center of the cover is that of Charles Babbage, which is on display at the London's Science Museum.
I was a little doubtful that the "pimp-cycle" picture was a nod to Johnny "Guitar" Watson's album What The Hell Is This? but now that I know that Johnny is hanging on Pearl Jam's bathroom wall (watch the video I posted this morning). I guess we can say that's where Tom Tomorrow or the band found the inspiration. Of course, Tom added Honey Rider, Raquel Welch, and a third hottie, who I have been unable to identify.
And speaking of that 10-minute Backspacer Promo, it's pretty clear that the person enshrined on Pearl Jam's speakers is features on the cover. You can tell from the hair style that the person on the TV in the pop-culture picture is a perfect match. Who he or she is, and what he or she has to do with Gilligan, Lost in Space, and Plan 9 From Outer Space remains to be determined.
That leaves us with four or five mysteries. Don't worry, as work continues, I'll bring you the updates! If you know something, don't forget; the discussion continues here.