Do not - do not - apologize for anything in this marvelous tale. I can't imagine stepping into my doppleganger's life on another world and having him in my head and give me a running commentary on my actions. Nor can I imagine Jonathan's pain - watching an almost identical stranger taking over my son's life. altClark is handling this as well as I could expect, and he seems to be dealing with the world's expectations of Superman very smoothly.
But he's under constant stress. altClark literally can't do anything without risk. If he makes a mistake in the newsroom, they can chalk it up to "the Krypton experience" and get away with that until the new mannerisms become ingrained patterns. But there will still be little things to indicate that altClark is an interloper in another man's life. The handedness is interesting, and it's interesting that Jimmy mentioned it. Cooking skills? "Had to learn to cook for my self on Krypton and discovered that I liked it." (Don't know if that would work.) The regular runs around the park. I only hope altClark doesn't go a little bit nuts from hearing Clark2 in his head all the time. Of course, it helps that the extra voice is both sympathetic and supportive.
All that makes me wonder how much Perry suspects.
Lois is still a hero. She's supporting the new Clark in her life as well as she possibly can, and even though she knows he's not the same man, she's opening her life to him. She showers and changes clothes while he's in the next room (very intimate), she writes with him as a full partner, she runs with him regularly, she willingly embraces him for both his comfort and for her own, and now she's kissed him on the cheek. And we all know that wasn't a kiss from just a friend.
I won't be surprised if Lois suffers a serious bout of unwarranted guilt when she realizes that she's replacing her Clark with this new Clark in her heart. It's the same kind of guilt experienced by widows and widowers who fall in love again, especially since she hasn't been allowed to grieve publicly for her lover's death. She may wrongly think she's a shallow and heartless woman because she's slipping into a new relationship with her dead lover's replacement. And she has few avenues for comfort here, since they can't tell anyone the truth without either destroying Superman and the world's future or getting committed to a mental institution.
This is a fascinating tale and I want to read the rest of it! And joy of joys, it's only the first part of a much longer story. I don't know where you're going with this, and that makes it fun for me to speculate and consider how I'd handle this premise. Of course, I never tried, largely because I doubt I could handle it as well as this. Keep it up!
