I sometimes use
PDFCreator which works as a printer driver but instead outputs a PDF file. The problem it appears to have solved is the one where a PDF conversion using Calibre loses the second of a double letter sequence and replaces it with a space. Like 'all' being converted to 'al '. This worked on my test of a PDF file that setting Calibre to 'keep ligatures' doesn't solve the problem, but using PDFCreator to create a second PDF file does.
Creating a new PDF first (using PDFCreator) then using Calibre to convert the new PDF to an ePUB seems to have solved the double letter problem.