it's been years since I read that part, but is Yahiko a possible answer?

would kind of explain Nagato and Konan's respect for Tobi, and iirc correctly there's no real proof he was killed (Yahiko could have just let Nagato take his eyes so that Nagato could show Danzo "evidence" that Nagato was dead)

I don't know if this doesn't make any sense at all, it's been like 3 years since I read the Pain arch

no because yahiko's corpse was the main Pain. and hes been said to be dead by several people

Nagato activated his eyes way before he meet Yahiko. The night his parents died.

would be cool though but its been made clear those three are good so even more proof it just wont happen