OK, here is the basic set up.

It starts off with Lois and Clark exploring the cemetary in "Bolt from the Blue" to see if they can find Luthor's body. However Mr. Waldecker does not show up, so Clark stays by Lois and in his Clark clothes.

For some reason (this is the part that I can't figure out, so you will have to in taking the challenge) Clark and Lois get struck by lightning, thus Lois gets Clark's powers.

What will she think though, since she got the power from Clark? Will she think he is SM, or will she ask him if he got powers from being stuck by lightning to? And if she asks him that, what will he say?

As a matter of fact, she might not even notice she has these powers until some time later...

But even if she sees the connection between the lightning and the powers - what will she make of it? Will she think that Superman isn't really an alien, but got his powers by being struck by lightening? Or, even worse, will she assume that Clark must have the same powers now and urge him to take up a new superhero identity, leaving him with a triple identity?

I agree that Lois getting powers from lightning might not be noticed by Lois at first, but the miracle of surviving without a scratch would be more obvious and immediate.

Well, I think Clark would probably have to tell her he is SM if she thinks he got the powers from lightning. There is a story by M. L. Thompson where Lois gets the Superpower from lightning while they are investigating the neo-Noah, and she wonders if Clark became Superpowered to. But that is in an alt-world where Clark works for the Star and is not Lois's best friend, so the whole thing is a mess.

Oh, that is also in a world where Superman has not gone public. I figure as long as you are in a world where Superman has gone public, if Lois gets the same powers she will figure there is some connection. She might figure Superman is a result of a different lightning strike, but she would probably confront him about it.

On the other hand, Clark might be so worried about how mad Lois will be if she learns he has lied to her, he might try the triple identity thing. He sometimes almost seems that lunkheaded.

Hmm, I just thought of another issue. What if Gretchen sees what happens are realizes that CK=SM, even if Lois does not. This would be very bad for CK and Lois.

VERY bad, unless Luthor dismisses Clark as a hack and demands that Gretchen find out how it worked (i.e. that the process just needs lightning because how could a hack like Clark have superpowers?) The reason I suspect Luthor believed the Cl-ois was because she was guileless and had no real reason to lie. Gretchen definitely might have reason to.