You're not going to like this, but I've found that the simplest, quickest, and easiest way to scan in multiple pages into a PDF is to use Adobe Acrobat Pro. There is a 'scan to PDF' option under the Documents menu in that App, and so long as there is a usable scanner driver on the Mac Acrobat will scan in as many pages as you want into PDF. It will even OCR them as well if you want.
The problem is that you must have Acrobat Pro. I don't know if any of the other PDF generation apps available for Macs will do this. Some of the non-Acrobat (that is, cheap) PDF generators on Windows do.
I use Acrobat Pro for all my PDF scanning, but then I had Acrobat Pro for other reasons. It might be overkill to get it for just one project.