Aaaaand Clark knows he's in trouble.
And in more ways than one.
Clark not telling Lois his secret because he needed to know if Lois loved him for him, not Superman... sure puts a kink in his loving her. Truth be told, I bet it's more along the line that when it came to Lois, he didn't have the self-confidence in Clark to tell Lois the truth, especially after he told her on the bench that he loved her (before she accepted Luthor's proposal); therefore, putting the blame squarely on Lois's shoulders is doing her a disservice and makes her sound awfully shallow (then, again, she did accept Luthor'r proposal when not being in love with him and being in love with Superman). This isn't a comment on your story per se, DC, but that plotline from canon in general. After Lois rejected Superman to date Clark is really when he should have told Lois. Big ol' chicken!
It's ironic that Clark used Mayson learning that he was Superman as a way to let her down gently. Although, it was tackless to say (while she's in the room) that the real reason he couldn't be with Mayson was that she wasn't Lois. (So much for letting her down gently).
I was worried about Superman being in the hospital until I remembered that he had been in the hospital before during Top Copy. Jeffery C. (the guy who answered the phone at STAR Labs), isn't he the guy who tried to develop a virus from Kryptonite? The same one who framed Lois for her informant's murder in Metropolis V. Lois Lane? You really did jumble up the timeline in this story.
I hope Dr. Klein can find out what's making Clark sick.
