Seeing where my files are used in FM ...?

Half an answer, or even less ... make a LoR for each book; at least that gives you some basic information to start from. You can then do a bit of manual tweaking to move that basic information into a spreadsheet; and I've heard it rumoured/suggested that FrameScript could be persuaded to write to a tracking document each time you add a new graphic-link to an existing .fm file.

I agree, though, it does seem to be something that's missing; I've had a similar problem with text insets. Making static lists can be done, even with wild and woolly solutions like mif/xml, grep, text-editor and duct tape, but automatically generating and maintaining them is something else.