awesome wfoley! Yes i think that is a great idea about the main story being shadow lord with a zilart ended; CoP with Apoc Nigh ending; all of wotg and abyssea. you can also do the add on scenarios, since they're independent of any other story and should be easier to write. using all of the in game dialog would make it easy to read and true to all of the people wishing to reminisce about ffxi. but honestly though, work on the story of the shadow lord first; do it first so you're not intimidated by the size of everything ffxi.
as for the main character, if you can make it so that the main character is genderless and jobless that would defiantly keep the feeling of reader immersion. It should be easy for at least everything before wotg, because your character didn't really interact much, people just barked orders at you and praised you for bringing good news.
do this and i fully plan to make any story you make as viral as possible.