I'm kind of surprised Clark wasn't more pro-active when she left. I know you tried to write him as patient but I always read his comments about "not letting this happen again" made me think he would have been searching hard for her and wouldn't have just stayed at work (likely taking time off to figure out where she went off to). Then again, that did sound a bit stalkerish (not a typical trait for Superman).

CLARK: No. I'm just worried I'm a jinx.
JONATHAN: A jinx?
CLARK: Yeah. Let's face it, ever since she's known me, Lois's been kidnapped, frozen, pushed off buildings, almost stabbed, poisoned, buried alive and who knows what else, and it's all because of me.
-"Contact" (You're not her jinx, you're her blessing.)