This is a really fascinating story, and it does show us a different possibility of where the original pheromone story might have been going.

The main theme of this part, I think, is that Lois and Clark are awkward and nervous about the situation they find themselves in. There is the fear that the other one will regret his or her decision to get married to his or her partner:

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He regarded her for several minutes, trying to decide exactly what to say. His dreams had been uneasy, but the theme that ran through them was the fear that Lois would decide that she didn't want Clark Kent, Superman or not -- that she wanted someone more sophisticated than her hayseed partner, as he had once heard her describe him.
And there is also another matter to feel awkward about - the fact that this marriage happened so suddenly, that they almost certainly consummated it very enthusiastically in their drug-induced haze, that they had been absolutely unprepared for such a development and that they are now at a loss at how to deal with that aspect of their relationship:

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She looked down at the rings on her hand and at the gold ring on the hand that Clark had slipped under her knees. They still had that decision to make, but for now they were just having fun, as he had suggested. Later, they could decide what to do about their marriage. It was doubtful that they could get an annulment, she acknowledged. Judging by their clothing -- or lack of it -- when they had awakened, neither she nor Clark could truthfully claim that the union hadn't been consummated. As a matter of fact, some of those memories were beginning to surface as well.

Best to not think of that, she decided. She had to stay sensible about this, and that particular recollection certainly wouldn't help her keep a cool head. She glanced quickly up at her companion, wondering how much of those three days he remembered. Probably more than he was letting on, but Clark could always be counted on to be a gentleman.
And Lois has really felt embarrassed about being near a not fully dressed Clark Kent in the morning:

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She started to speak but, at the sight of his towel-wrapped form, she froze, her mouth half open, and her eyes flicked from his face down his body and back up, lingering for an instant on his chest before she wrenched her eyes back to his face. She swallowed. "Uh ..."
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She reached out a finger and just barely touched his chin before snatching her hand back. "I guess you already -- how do you do that?"
And she just barely dared to touch his chin to find out if he had shaved.

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He caught the hand. "Lois, you don't have to be afraid of me. I'm the same person I've always been."
I love this. Clark feels the need to reassure Lois.

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"I'm not afraid of you," she said quickly. "It's just that I never expected to be looking at Superman in a towel." She was blushing more deeply, but he noticed that her eyes still strayed occasionally to his chest. That was a good sign.
No, she isn't afraid, but she is embarrassed.

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"I checked the sizes of your clothes and picked you up some things at the store. Do you know how hard you are to buy for with that build? It's a darned good thing that a lot of Hawaiian clothes are loose. I mean, you have a narrow waist, but your thighs are so muscular and so is your --" Her voice trailed off and her cheeks had grown positively scarlet.
Oh, this is adorable. Lois is unable to mention Clark's backside. That is how uncertain and embarrassed she is about the situation.

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"I'm flying over some of the most incredible scenery in the world," she said, "in the arms of the most incredible man in the world. And the most incredible part of it is that he's been my partner for months and I didn't see it."
But when she is flying with him, she is relaxed and happy.

Hmmm, Nan. I know that you don't write nfic scenes, and I'm not asking for one, honestly. But I do so hope that you will give us more than just a passionate kiss to solve the awkwardness between Lois and Clark and give us the feeling that they are now happy about being married. Personally, I don't think I will be happy with just a kiss. After all, Clark and Lois kissed off and on for three years on the show, and that didn't bring them a whole lot closer to intimacy. Being engaged didn't turn them into lovers, either. But now they are married, and if they are going to stay married, I want to see that both of them are ready to welcome intimacy. Like I said, just a kiss, even a passionate one, won't be wholly satisfying for me. You might show us Clark flying Lois into their bedroom at the hotel, and you could make them say or think enough to make it clear that they are definitely going to share the bed that night. That would do it for me. Of course... the end of this chapter spoke of the possibility of deserted beaches... that sounds just lovely!

I wouldn't mind if you make this a four-parter, Nan. I hope this story will end at a stage where Lois and Clark both feel comfortable about being married to each other. But I can see that they have quite a few issues to work out before that can happen.

I very much like this story, and I'm looking forward to more!

Ann