Are you committed to using Acrobat for scanned in documents? Is there a reason you couldn't use jpg (picture) files instead? That would solve that part of the problem.

You'd still have the issue of links to external websites.

As for directory structure...

I've just started using PAF so I don't know if this is 100% accurate.

At the top I have a directory called genweb. Beneath that is a directory "images" and "other".

I have jpgs of my various source documents and photos of people. Each type of source is in it's own directory underneath images.

The actual PAF program is in a directory "PAF-app" under "other" and the PAF data file is in "PAF-data" also under "other".

I can link to each image easily enough. Not sure though if the image is kept in the PAF database or just linked.

To share, all I'll have to do is copy everything under "genweb" to keep the relative paths. People may have to copy to their hard drive and change it from read-only, but that should be easy for all but the most DFUs.