Wow-- Lois reacted much the way we expected her to react. Considering how she was after Claude, she's likely to be even worse now. Even more brittle, defensive, and wary.
I liked how Clark originally felt like the wronged one because she kicked him out, but then went on to see things from her point of view. He had this looping thought process going on: his past life was over, Clark Kent was really dead; there was no way to fix this; he had to get away and stay away from Lois; he loved her so much; how could he leave her to dangers (real or imagined)... Then suddenly, he snapped out of that repeating loop and sort of stepped back and really looked at, really saw, the situation and his actions-- and for the first time he understands what has happened here.
I, too, wonder how you can fix this in only a few more parts. First, you've got to get them to actually talk. To do that they have to be in the same place. How will you get Lois to actually stay there?
Here's another thought-- even if they can talk, and Lois can let Clark explain, and if she can actually really understand his thought processes... there's still an awful lot to forgive, and they have to find a way past her feelings, his remorse, and the fact that Clark is still considered to be dead.
I don't suppose you're going to resort to some deus ex machina sort of ending, either, are you? No Superman-turning-the-earth-backwards-to-go-back-in-time. No Clark-dying-of-kryptonite-poisoning-and-Lois-discovering-she-can-forgive-anything-if-he-lives. No time travelers. No perfume to override Lois's inhib- er, wait, that wasn't the problem at all, was it?
~Toc