You're in luck!
I've recently completed the first version of the FB4.x app importer, and it's included in the latest build of FuseBuilder 4.1 Edition, available online. It's very easy to use, and does an extremely thorough job of capturing the circuit.xml and fusebox.xml code into a project file... the only thing you'll have to do by hand is Fusedoc at this point.
In order to make it as flexible as possible I've made the app importer file a standalone act_ file that you copy over to the website you want to import. Then just include it into the index file after the runtime include, and the app is ready to be imported.
The rest of the importing sequence is handled within the FuseBuilder GUI, in the 'Add a Project' form. You specify the URL of the application you want to import, including index.php or index.cfm, and FuseBuilder will take care of the rest.
I should point out that the app importer uses wddx to serialize the project structure, but I don't think this'll be a problem because it seems like wddx is turned on by default for most recent versions of PHP.
Let me know if you have any trouble getting this to work.