That's an issue with the PDF itself. PDF is a horrible format for converting or editing in any way, and it is also the worst format in regards to readability on an e-ink device. And if you scanned it, chances are your PDFs are nothing but a series of pictures.
If the textbooks don't have a lot of pictures, you may want to scan it into an ePub, rather than a PDF.
If that doesn't work for you, and your PDFs are NOT the aforementioned series of pictures, you can try
k2pdfopt which has various settings to make it easier to read PDFs on a small device. It can reformat double columns, cut off margins, etc. But I am fairly certain that none of it will work on an image-based PDF as is common with straight-up scans. You would have to edit the pictures themselves to produce any changes, there's no such thing as parsing the text and reflowing it. Though the margins
might work to crop out any extraneous space around the picture (not space IN the picture), if there is any.
I would seriously suggest using a tablet though, if you want to read PDFs.