"Since I read papers up and down up and down, and jump between sections, I wish there was a PDF reader that allowed me to split the screen like emacs, so i can scroll each independently."
To do this I simply keep the same document open in multiple PDF readers at once (I use xpdf) and stack the windows either next to or behind each other, using a minimalistic tiling window manager (I use i3).
I wanted to hack on Sumatra, and actually downloaded MuPDF, but, Mu only builds with Visual C++, and VCExpress wouldn't install on Windows XP for some unknown reason :-|
I did the same thing you're doing with Sumatra and Foxit, but usually I just take copious notes, specially to forward references. Then make a second pass at the document using my notes as guide.
My first thought was to suggest a tiling WM too, but you're on Windows - VirtuaWin (http://virtuawin.sourceforge.net/) gives many of the same benefits.
It gives you multiple workspaces and lets you configure keybindings for lots of UI events. I have alt+[1-9] and shift-alt+[1-9] set to "change to workspace N" and "move window to workspace N", respectively. At that point, muscle memory kicks in, your fingers know Emacs is always on workspaces 7 and 8 (or whatever), etc.
That'll make it easier to manage the tens of Windows that come from reading lots of papers side by side.
To do this I simply keep the same document open in multiple PDF readers at once (I use xpdf) and stack the windows either next to or behind each other, using a minimalistic tiling window manager (I use i3).