I haven't tried using calibre's mobi conversion utility much, so I'm not familiar with what k2pdfopt settings work best with it. Try adding -ppgs to the k2pdfopt command and see if that doesn't improve the situation. Even turning -n off should still result in a PDF with a selectable text layer, though.
Have you tried loading the PDF into MS Word directly? If you have access to MS Word, that may be a better way to go to convert PDF to mobi. See my
web page on the topic.