This way she couldn’t see his face turn the same color as his cape as he stared at her, his mouth hanging open utter humiliation.
I think that should be "open in utter humiliation".
It was clear to Clark that Lois still admired his alter ego. That was a good thing.
It is good he sees it that way and is moving past his self-jealousy.
It would make telling her the truth easier.

he wants to tell her the truth.
Of course, that really depended on whether or not he could remember how to fly. If he couldn’t save them from Nightfall, he would never tell Lois the truth.
How could he, after having her hero fail her in that way?
He still needs to learn that Lois loves both sides of him without reservation.
Actually, it would be best if he could remember how to fly, and go kick that Nightfall fragment to kingdom come.
Maybe if he thinks lots of thoughts of Lois it will happen.
He didn’t know how he would ever be able to face her or anyone again if, due to his incompetence, he wasn’t able to save millions of people.
He needs to accept the truth of her saying it is not his fault that he lost his memory.
She cleared her throat and set her hand on Clark’s chest. “You remind me a lot of him.”

she is about to see the truth.
“No matter what you or he does, I tend to forgive you both,” she said with a teasing nudge.
See, she would forgive his not saving the world from Nightfall.

another kiss.
Her chest brushed against his in a way that made him wish he could fly, just so he could get them up to his apartment all that more quickly.
Somehow I think if he does that she will not want to go immediately to bed with him. A-because she will be angry and B-she will insist he go stop Nightfall.
“As Perry just reminded me, it’s not who you used to be and do that’s important, it’s who you are now.
I wonder if it should be more "who you used to be or what you used to do". The current wording is awkward at best.
I forgive you, because there’s just something so pure of heart about both of you.”
Clark:There is only one of me.
OK, I doubt he will say that now, but it would be fun.
She wouldn’t be thinking either of them was ‘pure of heart’ if she could read his mind at the moment.
Well, as long as he only wants her, I think she will be OK.
He used all of his willpower to stop himself from kissing down her neck and concentrate on what she was saying.
I have wonder if it should not be "to concentrate" to match the "to stop" in the first part of the sentance.
Lois chuckled, kissing him. “It’s not true, Chuck.

she called him Chuck.
Superman has never, to my knowledge, ever wrestled Godzilla, and I know everything there is to know about Superman.”
Clark:Except who he is when he is not in the cape.
Lois:What? He sometimes disguises himself as someone else? Who?
Not everything, he wanted to say. He actually opened his mouth again to say just that,

He is going to tell her.
when she interrupted him to say that Godzilla didn’t really exist.
I guess sometimes Lois' ranting helps Clark.
“No, I was going to ask how you know so much about him,” he said, stopping by the door leading into his building. He needed to delay, and figure out some way to let Lois know that Cat was up at his apartment, but that nothing had happened. He needed to tell her the truth. It wouldn’t be fair to Cat to sneak her out, and it wouldn’t be fair to Lois to lie.
Good plan in theory. If Lois would give him a chance to say anything.
She shook her head. “I don’t know. When I saw him, and I just knew that he would change my life,” she said, a dreamy smile creeping onto her face.
Clark:Now I am getting confused.
Clark gazed at her and wondered if he had felt the same way.
Yes, although he had more clear memories of interacting with a Lois Lane.
“Here. Let me…” He scooped her up and cradled her in his arms. This position felt so natural, so perfect, it was as if his arms had been made to hold her.

He is holding her. Hopefully she thinks of the Honeymoon Suite and not Superman at this moment.
As he stared at her, a series of images flashed through his mind.

His memory is coming back.