Lisbeth,
Another alternative to consider is using a database publishing tool like Datazone's Miramo to convert the S1000D XML content to the unstructured FM files. It requires a bit of XSLT to map the elements to the Miramo mark-up. This is a technique used by a major manufacturer of the world's fastest trains to publish their S1000D content.
Depending upon your timing and volume requirements, there is a Personal Edition of Miramo available (currently, you'll have to ask, as the MiramoPE site is down) that can be used to prototype and develop solutions, as well as doing production in a desktop (non-server) environment.