This is a known issue and has been discussed here previously.
http://macos9lives.com/smforum/index.php/topic,5963.msg44486.html#msg44486In
your case, I suspect that somewhere in the "convoluted process" you described, you lost your ownership of the files.
OS9 is now "seeing" you as someone
other than the owner of the files.
Basically, you're in muck up to your neck.
So, if File Buddy works, thank the heavens.
If it doesn't, my first suggested procedure:1) Using the Tiger disc, do a fresh install of Tiger - yes, that means wipe everything and start over - but this time do two things…
2) Install the OS9 drivers with Tiger during the disk initialization
and partition a separate volume for OS9.
3) Install Tiger on one volume, and install
only the OS9 System Folder and Finder on the other.
* Try the next step with just a couple of files to see if it works
4) Restore some OS9 files
to the Tiger volume maybe create an empty folder to put them in
5) Boot OS9, say a prayer, open the Tiger volume and drag them onto the OS9 volume. If you can do that, you
should be able to open and use them in OS9.
6) If #5 is true, repeat with the rest of the OS9 files. If you can get everything dragged over and it all works, you can then reboot Tiger and delete the ones on the OSX volume.
If this fails at some point (and don't be surprised if it does) come back, describe what happened / what you see and we'll try again.