The very bloody solution to your problem, Tabris, is this:
1. Find your Fall Further mod folder in */Beyond the Sword/Mods directory.
2. Copy the Fall Further Folder.
3. Paste it somewhere that isn't the mods folder.
4. Rename the new folder recently made by pasting 'Fall Further Plus'.
5. Go through with the install for FF+, when it tells you about not seeing Fall Further 051, say ignore.
6. If a Fall Further Plus Folder has appeared from the install check to see if it is in the */BtS/mods folder; if it is, great; if it isn't, move it there.
7. Once the install version is in the proper place, move the renamed Fall Further folder into the */BtS/mods folder and tell it not to replace files; but if it asks, do tell it to merge folders.
That is about what I had to do to get it working for myself, I had a similar problem with the FF+ installer not seeing FF or BtS. Hopefully the instructions above make sense and work for you, FF+ is quite a nice addition after all.
PS: By bloody, I mean crude.
PPS: That should work; note, I have revised this post quite a few times and something may have gotten lost in translation.