nekokami: if you're trying to read PDFs on the eBookWise, why not read the PDF directly? I use a script similiar to PDFRasterFarian to convert PDF => images which fit exactly on to the REB 1100 which I have (alex_d also helped me to get image dilation working).
It's currently linux-specific, and if you're on ubuntu you need to do
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sudo apt-get install pdftk python-imaging xpdf-utils
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The script is at
http://puggy.symonds.net/~ashish/downloads/build-pdf.py
You'll probably have to change the script a bit, because the eBookWise has slightly lower resolution and cannot read in landscape. You will probably have to change line 67 from cropped.save to cropped.rotate(-90).save and remove the REB1100 specific stuff at the end.
I was planning on posting a generic script sometime when time permitted....