Oh, boy ... the roller coaster has climbed the hill and is starting to plummet again!
I actually liked their confrontation in the motel room. Clark needs to stand up for himself like that. He may not have been right in the "why" this time, but I think it was an important step for him, both in his emotional recovery and in his relationship with Lois. For his own mental health, he needs to practice acting on his emotions instead of burying them and being firm in what he says, and disagreeing with Lois is a safe way to redevelop that self-confidence. Which leads right into why it's actually good for their relationship -- he hasn't figured it out yet, but blowing up at her
hasn't destroyed her commitment to him. Once he figures out that they can disagree -- that he can even be completely out of line -- without her leaving him, it will help move them toward that "normal relationship" he is so convinced they can never have. It all circles back to the "trust" part of the story, which is really well done.
As for going to Smallville ... I'm withholding judgement until I see more of what you have planned. I think Lois's reason for taking Clark home is a good one; not only will it surround him with familiar things, he will be able to start contributing to their relationship by providing income and housing. The cover story, though? Hmmm.... My first reaction was that it will draw more attention than necessary, and that it has too many holes still to be believable. (Which Lois admits right up front, so at least we know she's still working out the details.) But I've been awed by your story-telling and plotting decisions so far, so I'm more than willing to see how it all plays out.
As for Phil Deller ... Yikes!!

I have no idea who he is, but the whole situation is very ominous. I see that others think he could be Moyne, but Wayne described him as a "young man". How old is Moyne, anyway?
In my mind, I'd pictured Moyne as being closer to Trask's age, but thinking back over what we've been told about him, he certainly could be younger. As Menzie's nephew, he could be similar in age to Menzie's son, and thus the same age (or even younger) than L&C. Yet he's clearly been an agent for several years, especially given how many assignments he's had go wrong and his body count. I guess I'd been thinking that since he'd been working at the prison for years, he must be older, but Lois has had several years' worth of experience at her young age, so ... I guess I need to update the picture in my mind!
Are we supposed to recognize the name Phil Deller, though? I didn't, but a comment above makes me wonder if I should have.
Things are heating up! I can't wait for more!
Kathy