The files cannot be distributed because of the copyright reasons. You cannot find them on Aminet either for the very same reason. You can find them on OS3.9 CD, though.
Anyway, here's a list of system files not included in Amiga Forever distribution (note that the list might be incomplete) compared to OS3.9 CD:
Note that most of the missing files are not needed anyway because they are either disabled in AmiKit and/or a replacement is installed instead.
Then there are files located in Amiga Forever's WBStartup instead of their original locations: