My imported documents are not correctly being indexed. If you were able to upload an ACP file with the proper XML and folder structure, I would think it would do the same. What you might try to do is the following:
1. Delete the index (and possibly backup index) folder specified in your dir.root parameter.
2. Change the index.recovery.mode=FULL in your custom-repository.properties file.
3. Restart JBoss or Tomcat.
4. Test search of keyword that appears in your document.
Hope that helps.