Alex -- great stuff. I just got my Reader yesterday after hearing about it for months from mobileread user "geekraver" (who I know in "real" life). Anyway, I've been testing out the software on Charles Petzold's free ebook ".NET Book Zero" which you can find
here.
I've found that for some reason, it only finds 1 page in modes 1 or 2 (and the resulting file hangs my reader), but if I use 3 (all the options) mode, it finds all 267 pages. Not a huge deal, I'll just use option 3 and pick all the defaults from now on ;-)