I restored a RaQ using raqbackup and CMU. Everything appeared to be correct. However, when I tried to FTP via WS_FTP, I received a permission error. I was using the user id created specifically for this site. I then created a new user id and still received this error.

Any ideas on how to correct this?

Check ProFTP's settings. I believe it's located in /etc/proftpd. Or search by typing in "locate proftpd" and find the config file. Open it and make sure the settings are correct.

Thats why the CMU utility sucks :(

Just copy the files into the correct dirs and make the virutal sites/users again...

That way you won't be bothered with the CMU utility