Honestly the "file" merge tool that comes with FTM isn't up to the task of merging trees with duplicates. It does have some smarts that try to help with the job, but I find that they're really not up to the task. My advice is that you manually and methodically merge. You can still use the file merge tool, but don't rely on it to deal with duplicates.
It will be a very time consuming task, but it'll be worth it when it's all done.