Here are a few pages of the original scan:
(can only be downloaded 10 times, so only grab it if you really want to play with it.)
My thinking is that perhaps this was just a very bad book to scan. I don't remember having these kinds of problems before and having much nicer looking scans.
I'm going to try something else later today and see what happens. I have to move my virtual machine (so I can run the software, all I have are Macs) to a laptop so I can get settled in someplace a bit more comfortable for long term scanning.