Вам нужно зациклить массивы permcheckfile и permcheckdir.
for site in $(echo /var/www/*)
do
for file in $(find $site -type f -exec stat -c '%a' '{}' +)
do
if [[ $file != *444 ]]
then
echo "$site/$file permissions are wrong"
else
echo "$site/$file permissions are correct"
fi
done
for dir in $(find $site -type d -exec stat -c '%a' '{}' +)
do
if [[ $dir != *555 ]]
then
echo "$site directory permissions are wrong"
else
echo "$site directory permissions are correct"
fi
done
done