Kathryn, I loved this part!
I liked the fact that, even though intellectually Lois had forgotten what had happened, she still had a sort of emotional memory. Like when you wake from a dream and you can't remember anything about it but you still have a feeling -- maybe happiness, maybe sadness, maybe axiety -- left over from it.
And then she trusted herself enough to follow her own instructions. The fact that she didn't remember writing those notes probably clued her in to something not being right.
And she saved Superman without letting on that she knows he is Clark. Which means that, from Clark's point of view, the lovely intimacy they are having at the end of this part is not just because he's Superman.
So why does Clark have a different reacion here than he did in the show? I'm guessing it's because, even though from his POV she did it for Superman and not for Clark, Lois rebelled against Luthor and realized what a wicked man he was. In the show all Clark knew was that Perry interrupted the wedding. But in your story it was Lois who obviously turned against Luthor. So that makes her the Lois he has always known and loved but has missed the last few weeks while this wierd stranger took her place.
Looking forward to the wrap up!
