Since the original story was found, I'm hijacking this thread.
I'm fairly certain I found the story in question at nfanfic.com.
Things I remember:
Lois and Superman making love
Superman waking up, leaving naked, falling asleep in his own bed, and waking up with no memory of the event
Lois discovering she's pregnant, and refusing to tell anyone who the father is
Clark finding his missing super suit in her apartment and realizing the dreams he's been having are memories
I've been looking for several days and I can't seem to find it. Help?