Hi, Bob!
I'm glad to see this up.
Poor Clark. He didn't really mean to let that slip, but I can completely understand why he did.
My first instinct is to insist that Lois would never be so taken in by Lex Luthor, but of course she would because she was (in the show). At least your Lois has more of an excuse for her confusion--between Superman kissing her senseless and Clark accidentally revealing his feelings for her--on top of the impedning meteorite strikes--she's got a lot to think about.
Your characterization of Lex was spot-on. He doesn't come right out and accuse Superman, so he doesn't give Lois the option of defending Superman to him. He just implies that things don't look very good, which is not something she can really argue with. Ooh, he's slippery.
I do hope she'll wake up enough to realize how creepy it is that he has a replica of her apartment in his shelter. Serious stalker vibe there!
This reminds me of a wonderful exchange from Caroline K's If I Were You:
"I had lunch with Perry yesterday, and Lex just 'happened' to be dining at the same restaurant. Perry and I had made those plans over the phone, Clark. There's no way Lex could have known about them unless he's...."
"Tapped your phone, bugged your apartment, had you followed," Clark finished for her, sounding grim. "He's probably done all three."
She stared at him. "You're not exactly making me feel better here."
"You're being stalked by a sociopath, Lois. I don't know how to make you feel better about that."