I agree with the assesment of how alt-Clark feels for canon Lois. If I remember correctly she kisses him on the lips when he first sees him, and then he has to explain to Lana that he has no idea who this lady who came up and kissed him was.
I am not sure if Lois realizes he is not her Clark at that point, but since he looks exactly like him, and acts mainly like him, it is not too surprising a reaction, especially if she is not sure she will ever go back to where she came from.
