Anagram: Final Fantasy.
Sefyr, as you know, was clearly Sephiroth. Also from that game were Vincent, as Chase, and Cloud, as Claude.
From predecessors to that game in that series, were Sabin Rene Figaro as David, Rydia of Mist as, well, Rid Ya, and Bahamut as Hen Ri. The ninja Edge's six jutsus, Flame (Shane), Flood, Blitz, Image (Imidge), Smoke, and Pin were all present, but you did not speak with all of them.
From Lunar: The Silver Star Story, Alex of Burg as Alex and Mia Ausa as Mia; I determined the reference so obscure as to not warrant changing their names.
From Chrono Trigger, Janus as himself.
From Shadow of Destiny, Homonculus as the great demon at Demon's Rock.
From Rurouni Kenshin, Kenshin as Ken.
From Akira, Tetsuo as Tatsume.
From Dynasty Warriors, Guan Yu as Seiryu.
I don't think I missed anyone; I believe all other characters were developed by myself. Fizgig Blade Pain Skellie Vize Aegis Mark Nic Jewel Eria Jonny Reim The Mooks Ursana Moon Crescent and I suspect many others.
Of course, there were a lot of people you didn't meet; but that GE roll and meeting Eria that early, + meeting Aegis, +a few beastly an mag checks with Fizgig on top of some good GE rolls, really threw off the story.