A couple of pretty simple bash commands for finding and changing permissions on all files and directories recursively. Obviously you need to understand what permissions you want in advance so check the man pages and online but for when you find a load of files and directories have wrong permissions.

find <path>/ -type d -not -perm 775 -exec chmod 755 {} \;
find <path>/ -type f -not -perm 664 -exec chmod 644 {} \;