I don't understand why you'd want to convert these from PDF to another format. For a highly technical book, PDF is the best format to use, and the Kindle DX reads PDFs natively.
(I actually think PDF--if properly made--is the best format period, but I guess that has few adherents around here.)
If you want to remove the margins to make it slighty easier to read, try
soPDF. If you want to split the columns on to separate sheets, try
PaperCrop.
Acrobat Pro will not do a good job with the kinds of books you're talking about. Actually, nothing existing will, and it would be unreasonable to expect that anything should.