Alfresco 4.2e uses PDFBox 1.8.2, while the new 5.0a uses PDFBox 1.8.4, so one easy option is just to upgrade to a newer Alfresco release!
Otherwise, to upgrade Apache PDFBox you generally need to upgrade Apache Tika too, and that means upgrading some of the other dependencies as well. For extra fun, Alfresco are currently shipping custom patched versions of Apache Tika, so you might be better off grabbing the newer Tika + friends jars out of 5.0.a or HEAD rather than trying to find + replace the jars yourself. For the list of the dependency jars, you'll want to look in the Tika Core and Tika Parser poms.
I'd probably suggest the upgrade to 5.0.a, unless you have very strong reasons to stick with 4.2