Killy only lost like seventy percent or so of his biomass. That's pussy shit for him. Fourteen years of regeneration is a blink of an eye when you've been alive as long as he has.
Since in BLAME!, your "mind" or otherwise your identity is obviously based on nothing fancy like souls but simply the arrangement of atoms inside your head, as I suspect it works in real life, then you can pretty much assume that technically it was not Cibo but that since it was originally Cibo's structure that was corrupted by the safeguard data downloaded into it, it would be somewhat similar to Cibo.
The level 9 probably broke down due to confliction errors with the original Cibo's data and maybe interference from the Authority, Sanakan, Seu's genes plus whatever the hell else was in that orb, etc.
The builder at the end, I always assumed was somebody we know remotely operating it like Sanakan or Killy or the Authority, trying to protect Cibo and the orb.