hmm... i should've realized that autocropping won't really work. Because of the manual way I tell ghostscript how big to render the pdf, all the pages of the document have to be the same size.
Besides this, autocropping leaves behind a lot of stuff that's better off cropped. It does bother me that this adds manual steps, but the best result is to just go into Acrobat and set a cropbox for all the pages. For the Scientific American I'm using as an example, this worked really well. This magazine always sticks the actual text within a 7.75"x9.75" box, but usually has various other bits of crap going all the way to the edge.
After I edited in Acrobat, I then used the -dUseCropBox flag in ghostscript and changed resolution to -r82x81 (to enlarge and stretch a little horizontally).
To batch invert colors, I issued:
convert "out*.png" -negate "out%03d.png"
convert is a command you get after you install ImageMagick.
the weird characters in the filenames are there to get the numbering correct.
Result:
PNG - example 2d - Final Result
Compared to the original:
PDF - example 2
It is simply night and day. (pun intended)
I can now comfortably read full A4 pages on the Reader (in portrait mode!), justifying the purchase for me. I think others will feel the same way.
What's left is to figure out how to organize the PNGs ($#@#$ sony) and to simplify all this with a nice interactive batch-script wizard (or better yet a VB gui) and a howto. (I know the command lines must have really scared some people.) Lastly, this all needs to be extended to landscape mode which many people will likely prefer. (just render at 800x1128 or so, and split in half)
Also, to edit the cropbox in Acrobat I had to remove PDF security using PDF Password Remover v2.5. (The same thing can also be accomplished by creating a new pdf in Ghostscript and copying in the old one.)
P.S. I'm really not sure about the 768 vertical height. Just to be on the safe side, I'm using 764 so I can know that there is no resizing since I can see the extra borders.