He gulped, and she saw his gaze dart away from hers and down her body for a split second. “My gift?”
Oh, I was so hoping he would go for the possible meaning here.
“Right, my gift,” he said.
Lois:This would be so much fun if I was not about to brake up with him for his own good.
Lois could tell he was distracted from most everything else with her so close, and she decided to press her advantage. “Unless you want to kiss some more?”
Sounds like a good plan.
“Uh-huh,” she murmured, resting her lips to his and kissing him again.

more kissing. This is so much better than I thought this part would be.
[Quiote]She bet. Being that Clark actually was Superman would mean he'd have ample opportunities to test the claims of the pen’s manufacturer.[/Quote]
I was going to wonder if this might give away that she knows. However since she did not know when she bought the pen, I doubt it.
Lois gave him a soft kiss and jumped to her feet.

more kissing. We have exceeded Season 1 canon kisses in just this part. I just went and learned we are in a new story arc, that is evidently about to finish. That is inpressive that you cut ASU into two story arcs. Although this is technically later than anything in ASU.
“I do have another gift, which I bought first,

she is going to give him the big box.
but I thought it was a little silly, and…”
Or maybe not. "Silly" does not sound like her other reactions to it.
Clark needed her to get the man who tried to kill him behind bars and the Kryptonite disposed of safely.
She really is dead set on breaking up with him for his own good.
Lois wouldn’t be able to do that with Clark holding her back, and she knew if he knew what she was doing, he would try to stop her.
I guess I have to concede she has a point there.
She needed to keep her thoughts and emotions hidden;
This whole plan just does not seem a good idea.
knowing that if he wanted to, Clark could easily glance through the wall and see her having an emotional breakdown.
Clark:I would never invade Lois' privacy like that.
Lois:So you have never looked at me through a wall.
Clark:Well, OK, maybe once, but I really try not to.
Lois:So you would do that.
Clark:Not any more.
Should he be gentlemanly enough not to do that, he would be still be able to hear her.
I guess she has a point there.
Therefore, she had to calm herself while under disguise of searching for this ‘other’ gift, and do so silently.
So this gift is really the same gift, not another gift at all.