I store a lot of research papers in Calibre.
Most papers come in the standard 2-column layout, not optimal for reading on Kindle. I have found the k2pdfopt (
http://www.willus.com/k2pdfopt/) convertor good for optimising djvu/pdfs for kindle and also smartphones.
I would like to retain the original pdf along with the optimized one but calibre allows only one pdf to be stored for a book. Is there a way I can keep 2 differently formatted pdfs for the same book?