I think it's clear that Zod *isn't* controlling Lex until the actual download of Zod's spirit via the opening of the portal (otherwise, there's no reason to bother with opening the portal in the first place if Zod could just exert influence once Lex had superpowers).

During the Lexana scene I wasn't sure, then after the actual "downloading Zod" scene I agreed with you--I guess I'm just confused as to why on earth Zod would have gone to meet Lana on the rooftop of Luthorcorp. That's what made me wonder, well, that and Lex's earlier weirdness, but you're right, that could just be coming to terms with his powers.