In FileMaker 9-11, the best option to store files is to use SuperContainer.
To concatenate pdfs, check out Matt Petrowsky's site, http://www.filemakermagazine.com. You've got to pay to access it, but it's well worth it. There's a solution on there using another SuperContainer plugin called ScriptMaster and Java code. It's definitely an Advanced technique, but it's the only way I found to do the job in a reasonable manner.
I wish there were better options out there for manipulating pdfs and would consider hiring to develop a plugin.
I suspected this was the situation since extensive googling didn't bring up any other sources than references to Matt's video on filemakermagazine.com.
Here's a link to the article/video for people finding this thread in the future: