Nice story, Alicia!
I think it puts a good perspective into Clark's thought processes. He doesn't ever think that Lois could reject Superman but accept Clark. Even in his own thoughts, his alter ego is tied into his "real" character. So when Lois says she only wants to be friends with Superman, he thinks she is saying "I only want to be friends with Clark."
As for what's missing? That's hard to say. I think it works wonderfully as it is. If I were to say there was some ambiguity, I would put it in the reactions of Clark's parents. You didn't explicitly say that the continuity matches that of the actual "Whine, Whine, Whine" episode where Clark very early on says he wants to leave Metropolis since he has no chance with Lois. In your version, it seems Clark has decided while in flight to leave Metropolis. So Clark's parents wouldn't know this. Yet their warning to their son when he walks in on them and Lois is that he really needs to hear what she has to say before he opens his big mouth and messes everything up. It's as if they know Clark has heard Lois tell him that she only wants to be friends with him. Without that knowledge, I would think the Kents would tell him in a very upbeat way that Lois has great news for him or something like that. That's my impression.
