SQD, interestingly heart-wrenching story. While I do think there are a few minor problems, the scenes you portray are very powerful in their emotional impact.
I do think you need to better state the situation of Clark's powers better. You gave us your explanations in the comments folder, but it needs to be in the story. Clark, apparently, has had a lot of time to think, so I'm sure he's come up with many theories as to why his powers have never come back even though he knows the kryptonite is gone. There is no hard and fast rule as to how different levels of kryptonite exposure affects Superman, but your story's rationale needs to be better outlined within the framework of the story.
I, too, was confused as to why Clark is still alive, but you claim that that question will be answered, so I can wait.
A good visual of Clark; dirty, emaciated, and just a tad 'round the bend', as he lives through his writings. It's been a long time gal, we need to know what's been going on with Lois.
Tank (who thinks that Lois may have slipped into a daily life routine by now, but he needs to see her progression from faith, to loss and acceptance and a hollow life)
