/etc/project isn't supposed to be executable (should be 0644) but I wouldn't have thought that would actually cause your error...

Why not just recover the correct permissions from your backup's Table of Contents, then reapply them via a scripted chmod? That way you know you've got everything back the way it should be.
What's your backup software?

Alternatively, use another v440 sol9 build to provide you with the correct template, use the find command on the two systems and script a lookup to calculate the correct perms.

Let us know if you need a hand with these, it's a relatively straightforward problem and to debug each seperate issue one by one will have you busy for years - not to mention introducing questions about what caused it on every bug or issue you find on that box for ever more.

BTW, running chmod 0777 on anything is always avoidable, the only time you'll ever need 777 rights on a directory is when you'll also need the sticky bit set too.
Using a -R suggests that your admin was trying to solve a permissions problem by just making everything full rights; including execution rights which you never want on a data file (imagine if you accidentally ran it, you'd be piping random bytes of data at an interpretor, the kind of mess that could make is horrible).
Aside from the mistake over where to run it (that happens to everyone at some point, I've seen a recursive rm ran from /, I've had a chown -R go very wrong myself), I'd say you should be having a talk to them about security and safe practices.