Assuming you've created a text file named "ordered" with the PDFs in the sequence you'd like to create:
$ cp /System/Library/Automator/Combine\ PDF\ Pages.action/Contents/Resources/join.py /usr/local/bin/join-pdfs
$ perl -e '$first = <STDIN>; chomp $first; while(<STDIN>) { $index++; $intmdt = "foo$index.pdf"; chomp; system("join-pdfs -o $intmdt $first $_"); $first = $intmdt; }' < ordered
Now you'll have a host of foo.pdf
files; the last one is the one you want to rename to something useful, then rm foo*.pdf
.