I would like to automatically generate PDF documents from WebObjects based on mulitpage forms. Assuming I have a class which can assemble the related forms (java/wod files) is there a good way to then parse the individual forms into a PDF instead of going to the screen?
The canonical response when asked about PDFs from WebObjects has generally been ReportMill. It's a PDF document generating framework that works a lot like WebObjects, and includes its own graphical PDF builder tool similar to WebObjects Builder and Interface Builder. You can bind elements in your generated PDFs to dynamic data in your application just as you would for a WOComponent.
They have couple of tutorial videos on the ReportMill product page that should give you an idea of how the tool works. It'll probably be a lot easier than trying to work with FOP programmatically.