[ldolse]

You shouldn't have missing or garbled words unless the original was messed up. The main problem with pdf is you lose some formatting and you'll see the occasional hard line break.

If there are accented characters this may give you the impression some text was garbled - use the 'Keep Ligatures' option under look and feel to fix that.

Edit - Your pdf might be images with OCR underneath that. That would cause you to think the pdf was good, but it's only because you can't see the bad OCR underneath, which is what Calibre would use. Find some of the garbled text in Calibre, then go and copy the same text from the pdf, and copy/paste it into a text editor. If the text editor mirrors Calibre then you can be sure that's the problem.