More progress, and some regression:

• I can't get RVDB's Ant script to run; it dies early in the process claiming that it can't find a build.sh file which is obviously there. Rather than struggling with Ant, I've decided first to go back and work from my own script, and integrate RVDB's steps (the ones we want to keep) into that. Later, once I understand it all and it's working, I can think again about rewriting it as an Ant task.
• Both FOP and Cocoon 2.1.12dev are pretty static -- no changes for a long time -- so I'm not going to worry about checking out fresh copies of those as part of the script.
• I have my script working up to the point where the FOP Jars are copied over into the Cocoon lib directory, but I haven't yet implemented the required changes to the Cocoon jars.xml file yet. I'm looking at a range of changes RVDB is making through his exist-gump.xsl and exist-jars.xsl files, to patch gump.xml and jars.xml, and I think I'll have to take those and modify them so that they include the other changes required for FOP, which are documented here.

This is going to be a long slow process, but by the end of it I'll have a clearer idea of the changes that need to be done and the reasons for them. That will help when it comes to integrating the Analyzer patch.