I was just thinking, as your story is stuck on my mind now. What would the Lanes think of Lois's disappearance? And the police? Would Clark be accused of her murder and/or disappearance? I can't believe that they would take "she walked into the bathroom and disappeared" as a reseasonable explanation. (Certainly not Ellen!) Nor could would they believe about Tempus or the time window. Poor Clark.
You torture him so beautifully.
Did John Doe still come and steal Superman away and try to take over the country and Herb... oh, no, I guess that didn't happen because Clark never saw Herb again.