10.4: Use Automator to combine PDFs - Mac OS X Hints →
10.4: Use Automator to combine PDFs
Insert the Automator action “Finder / Sort Finder Items” and select the criteria to sort on. You can sort by name, time, keyword, label, etc.
So you workflow would be:
This assumes that some form of sorting of your files delivers what you want your final PDF order to be. If not — check into the Automator Finder Rename route.
—drewk—