I don't think I have it in me to write a story like this, but this has got me thinking. What would Clark be likely to do different, especially immediately?
1. I think he'd go to his parents and pitch his Superman idea early and have Martha make the suit. This time he has the final design in mind already.
2. He might not wait for the shuttle bomb thing to debut. Maybe he saves the Messenger shuttle. He might figure that if Lois is not the first one to see him in action, and if he doesn't fly her gallantly into the newsroom, maybe her crush won't be as bad.
This could have some potentially far-reaching side effects. If Lois is not the first reporter on the scene, whoever is there might not have quite as favorable a spin to put on the news coverage. It really could go either way.
3. Before Superman shows up, break into the warehouse on Bessolo Blvd. and take his ship. Bureau 39 wouldn't be expecting it, and I'm sure he could do some surveillance and find a way in and out without being caught. While he's at it, take some random files along with the Smallville ones, just to throw things off a bit.
4. Have his dad talk to Wayne Irig about the tree. He's got to prevent Wayne from sending any samples of any as-yet-unfound interesting minerals to any labs for analysis.
5. Write down everything he remembers about Luthor's crimes any any evidence that he collected the first time around. If any of that exists yet, start getting a hold of it. If it hasn't happened yet, Clark's got the upper hand and will be able to obtain evidence in a more timely manner when it does happen.
6. He will really have to watch himself around Lois because he knows her much better than she thinks he has reason to. He has to remember not to say anything that would give her reason to believe that he has more information than he should (e.g., mentioning her relationship with her dad, being familiar with the layout of her apartment, knowing that her sister is staying with her, etc.).
If he changes things enough, especially if he finds evidence on Luthor early, things won't unfold as he remembers, but I'm sure he'd still be on the lookout for, for example, Miranda. Maybe he couldn't find a way to prevent her from spraying the newsroom, but he decides to take Lois up on her offer of playing hookey before Lois gets sprayed.
Anyway, there's my brain-dump on the subject.
