She kept him on his toes, constantly surprising him, not necessarily in ways that he liked, but often – as with both of his birthday gifts
I wonder how happily surprised he would have been if she had given him the other gift.
and how she wanted to hear about his amnesiac fantasy about Meena
I still have severe doubts it was a fantasy at all.
which he could happily spend his entire life trying to understand.
I am glad I do not have as much despair for their relationship working as he does. I was hoping her lines about "temporary" and such would convince him to not loose hope, but I am not seeing that happening.
Clark already missed her kisses,
He really has it bad for her.
That makes more sense, although they never touched much in the newsroom.
and even her glances at him from across the room.

that Lois is at the trial.
Okay, they still shared those,

for shared glances.
“Did Lois tell you what happened yesterday?” the Chief asked. “Why she froze?”
Not the real reason.
refusing to allow Lois to get a bad rap from missing the Superman exclusive due to his own weaknesses.
Well, I don't think that is the real reason she missed the story.
This is such a complexed interaction. Perry knows more than he is letting on. Everyone knows CK=SM, but trying to pretend it is not so to the others.
“Did she? I hadn’t noticed,” Clark replied, focusing on the screen, so Perry wouldn’t worm out of him that Lois had been anything but cold with Superman.
Perry:Now what is he trying to hide?
He never knew making out with Lois while he wore the uniform could be so hot.
Probably good he did not try it sooner, otherwise she might never have come to love Clark.
“You didn’t interview him at the same time then?” Perry asked.
Clark cleared his throat at that physical impossibility.
Actually it would be possible. Just not easy while keeping Lois unaware of The Secret TM. Although some people think that Clark can pull off the allusion of being two places at once. Hmm, he could always use a hologram.
“Uh-huh,” his boss replied, studying Clark.
He is trying to decide if Lois really was right.
Mostly because she wouldn’t like him covering for her in this way.
He needs to learn keeping secrets from Lois is always a bad idea.
When I didn’t call, she slammed me for it.”
If he would only learn to always call Lois.
because her description would have been the closest.
I wonder if this line really works. Closest to what?
“Maybe what you need is a few days apart,” Perry suggested.

bad idea. We like Lois and Clark together.
“Let her cool down. Why don’t you go visit your folks in Kansas? Get yourself out of Dodge, so to speak, and away from the giant target painted on your chest… back!
This does sound like a slip from Perry knowing that CK=SM.
Perry nodded. “I’m sure they’d love to see you too after your ordeal. I take it flying isn’t easy for them?” Then his boss made the oddest expression. “Plane fare being so expensive and all.”
Perry is trying not to say "like it is for you".

there is hope for him yet.
Martha took a sip of her coffee. “Do you think she still has feelings for Superman? Did she officially break-up with you to see if anything would develop there?”
Oh no, that is that last idea Clark needs suggested to him.
“I don’t know. She said that she loves me, but that she needs time to work something out.
I have fears about where this is going.
She said it was only temporary, and I should trust her.”
That he really does not do enough yet. He still needs to trust her more than he does.
“She told Superman that even though she loved him, she was in love with Clark, and that there couldn’t be ‘us’ – a ‘Superman and Lois, us’.” He scratched his head. Had she changed her mind? “I don’t know. I really don’t know.”
That really does not sound like she is thinking about trying a relationship with SM.
“You’re right, Superman, one kiss changes everything,” Lois had told Superman after their first kiss.
Fortunantly that is not what she meant.
“Yeah,” Clark murmured, cringing from the very thought. He had built up a relationship between Clark and Lois for the last six months, since Superman had taken Lois into the mountains and broken up with her, only to destroy everything with one stupid amnesiac kiss.
I just have this thinking fear he will do something that will make everything worse.