I have relatively sensitive data in .docx, .xlsx and PDF files that all need to be converted to a single PDF file locally. Sending these files off to phpdocx or Google Docs or anything like this is not an option.
The only other option I am seeing is OpenOffice / LibreOffice but I am not satisfied with how they are converting the documents.
Is there any other alternative anyone is aware of? Thanks!
Definitely a difficult task. The very recent release of LibreOffice 3.6 has fixes to it's docx processing if that might help, but you haven't specified what the actual problems you encountered when you tried OpenOffice.
If you have time to experiment (and bring in any tools/languages you need to get the job done) you could try LibreOffice to produce PDFS, then use one of the many PDF libs to stitch the PDFs into the single file you require.
You could also look at ODFConverter which has traditionally been much better with DOCX than either OpenOffice or LibreOffice. This would allow you docx -> odt -> pdf. I think it can do the xlsx also. Then do the PDF stitching again.
I suggest testing the stages manually at first and if promising, try something like JODConverter (requires Java) to allow you to automate the process via scripts.
Good luck.