the first step says I need to DL the torrent and install ffxi, but if I have the fffxi retail version installed can I just skip that and continue?

You will need the update files. The FFXI and expansions installer should be fine from where ever you get them.

SEE: http://nasomi.com/download.php

There is a section for people like you. "If you already have FFXI and ALL expansions you can download these only."

If your retail copy is up to date then you dont need to do anything other than use ashita. To manually force an update go into your FFXI folder and delete vtable.dat then load up playonline like you were going to play retail and check files for FFXI, it will see you are missing one grab the latest update for you.