Install was working; Update failed so I did a manual update and now it's broken

I was having trouble doing the automatic upgrade so I tried to do it manually by FTPing the files up. Now that I’ve gotten that there I’ve somehow knocked out the ZendId execute Permission and I can’t seem to get it to work.

The two directories it wasn’t letting me copy over was doc and devel so i deleted those directories and re-copied from the latest install and that’s when the problem started.

Any help would be great!