On the other hand, I know what he thinks of you, and what you think of him.
Clark:So are you just trying to make me jealous. What is you point in telling me this?
I don’t know how to meld these two contradictory parts warring inside of me.”
This really does make it sound like she has positive feelings for Lex despite the negative feelings that Clark has towards him. Even knowing what I do, that is still the only way the last line makes sense.
She laced her fingers together and shook them in the air. “Oh, Clark, I’m totally flummoxed, and that’s not a feeling I like. I need you to look at this clearly for me.

Clark let her. Let her speak again and clearer.
Clark didn’t know how much more explanation he could take.

lunkhead, let her speak.
Did he want to hear how Lois had fallen in love with Lex?

has she said one word of love. Has she praised anyone but you Clark. Listen to what she actually says.
No. Did he want to hear how marrying Lex would also be good for her career, because of his connections? Nope.

Clark stop assuming.
Did he want to hear how she loved Clark, but how Lex would be a much better match for her because of his social status and wealth? Certainly not.

stop treating Lois as if she is super shallow Clark. She fell in love with you as Clark, not just you as Superman. She loves you. Aargh, why can't he see that.
Taking Lois’s elbow, Clark led her to a nearby bench and invited her to sit down.

at Lois for not trying to start he explanation again.
He felt he must do something, but he wasn’t quite sure what.

Clark, you don't have to do anything. Action is not what Lois needs now. She needs a friend to listen to her concerns. Be that friend Clark.
He knew he had to say something or she would make the biggest mistake of her life,

No Clark, there is nothing you can do to make things better except listening to her.
Then tell her to not marry the murdered.
Finally, he came to a decision.

at Lois for sitting quietly and letting him do this, when she said she needed to start over.
He would tell her the truth and let her make an informed decision.

at his off the wall understanding of what "the truth" is.