Of course my answer is "Try it on Ubuntu". I setup my HP all-in-one officejet scanner using a simple setup utility over ethernet. The FI-5120C is fully supported by the linux SANE project. (http://www.sane-project.org/sane-mfgs.html#Z-FUJITSU)

I wrote a simple script to scan many documents, do some simple processing and write them out as PNG. I suppose it wouldn't be difficult at all to convert the script to support output as PDF instead.