I love the way you keep taking this in unexpected directions, the way you keep us guessing. It is not at all cliched or predictable, and is a great read. Thank you!
It's pretty clear that Clark is not going to confess if he can help it, and that Lois is not going to figure it out without lots more evidence than she has now. As someone else rightly pointed out, Clark should be impossible. So my bet now is on Clark using his powers in front of Lois, either floating in his sleep, or escaping from the Feds, or something else like that. You'll probably surprise us on that too, though.
Poor Clark is really in bad shape emotionally, as bad as Lois. I think it's going to take a while for them to trust each other.
“Does your world still have passenger pigeons?”
Too tired to even wonder why she was asking, Clark said, “No.”
Uh oh. That doesn't sound like a good thing. I'm guessing that their problems just got bigger than Clark getting home.