I understand Rei put the spear in it in episode 14, but how did Lilith get up there in the first place? I doubt there's a concrete answer, but I'm just curious. I've always assumed Nerv just put it up there since it was already in the Geofront. But I dunno honestly.

Seele seem to be either direct descendants or inheritors of precursor race technologies, so them doing crazy things off panel is somewhat normal. I wouldn't even be surprised if, rather than putting it there, they simply grew the body right on a cross.

It was the Romans.