yeah a clone is a possibility but i think that mana may not even be human anymore. i remember that gai said something about living inside the crystals being the next stage of evolution and i believe that's how mana was able to continue living in a form (the crystal wedding ring belonged to mana). thats probably the same way gai was able to be revived. probably like a hauxcrox from Hp Lol. or maybe they continued through the apocalypse virus.
or maybe a suitable person has to be a void genome compatable person or have a similar void to manas. though i believe a clone would be the most logical assumption I'm not sure it's that simple. though you are probably right with the clone theory
anyway back to the not human theory i believe that inori wasn't human either, due to her state before she was captured and the fact that all the GHQ members were insistent on the idea that she wasn't human. though that could be just mana's consciousness doing the work and the members could just think clones aren't real humans. though she is defiantly said to have been 'created' and has no parents. though if mana was really human then that doesn't explain why lost christmas happened. but whatever this is getting us no where.
Either way, it would have been nice if Guilty Crown had bothered to explain the backstory and creation of one of its main characters. Otherwise, it's hard to care about the character when all she does is yell the main character's name.
It's Ouma Shu's love for her that gives her a place in the viewer's attention and affection. His devotion, and hers too, and how she sacrificed herelf up to simply save him. I think it's quite obvious Yuzuriha Inori is neither clone nor human. She is a replica, a created body that would be compatable with the consciousnes of Mana and was never meant to have a consciousness of her own. This is why she calls Tsutsugumi Gai her saviour, he pulled her from the hold, forcing the body to gain a soul.