If I were in your shoes, I'd probably try
PDFread to convert to PRC format, which should result in output that looks just about exactly like the original PDF. I think the tradeoffs will be that you'll lose dictionary support and searchability, and have larger file sizes.
You could also try Amazon's Kindle PDF conversion service, or the PDF converter in the MobiPocket creator, but I'm not sure you'd get better results than with calibre.
There are some similar tools that I like even better, like PDFLRF, but that won't give you output directly usable on your Kindle. (I suppose you could use PDFLRF and then use calibre to convert the LRF to a .mobi, however.)