I don't have a single funscript in each directory, my layout is as follows:
\media\videos\A-M\*
\media\videos\N-Z\*
\media\funscripts\A-M\*
\media\funscripts\N-Z\*
Plus a couple more in that format, so it just keeps things a little cleaner. It would be nice to just copy the media\funscripts folder to the quest and have it pull everything recursively from there. Not a big deal, just something on my wishlist.
Thank you though for a great project!