38. In MoSB, while Lois is getting out her pasta sald and Superman is putting water from his tea kettle in his hair to make it look like he just got out of the shower, Lois turns around and notices it. She realizes that Superman was not in the shower, and thus after thinking a bit it makes sense that CK=SM.
39. When discussing the train in MoSB Lois says to Superman, "Clark and I will meet you there."
Instead of making some lousy excuse that makes Clark lookbad, Superman turns to her and says, "No you won't. I am Clark."
40. In MoSB when Superman is telling Lois that he has to leave in the court house, he touches her. I am not sure if we ever saw Clark touch her that way before, but I am assuming even if we didn;t see it in GGGoH, it happened. So she realizes that SM=CK, and then when she sees CK in the newsroom paking up she confronts him with this information that she knows. She is also able to convince him to stay and help her get to the bottom of the mess.
