Looks great so far. Thanks for going the extra mile on the formatting!
A lot to talk about so just going to fire off some points:
For now don't worry about...
I wouldn't worry about Catalyst / Inhibitor or Unique Ability / Critical Flaw just yet. They can be fun to think about sometimes, and sometimes you'll get one that totally seems to fit, but often they don't become clear until later.
Cost is a price they pay in order to pursue the Story Goal. So maybe they're doing things that have a negative impact on their futures (future friendships, giving up their idea of what their future was going to be, etc.). Unlike Consequence, you'll see these negative things come to light throughout the whole course of the story.
Regarding the Holistic MC, just be aware that you'll have to write a holistic character, which might be challenging if you're a more linear thinker. Also be aware that it will appeal to a smaller audience (because holistic thinkers can still make sense of linear thinking, while linear thinkers often go WTF? at holistic problem-solving). See here: https://narrativefirst.com/articles/predicting-who-will-listen-to-your-story
That said, The Matrix appealed to plenty of men despite being Optionlock-Holistic, so do what you want.
I think you have your MC throughline totally nailed; the Domain and Concern fit much better than you may realize. Definitely use the original terminology for Innermost Desires: Subconscious. I think he has subconscious grief and guilt over his brother's death that ties into his denial of self, denial of his destiny, etc.
For the Relationship Story, throw away the idea of it being a battleground or argument between them, and just think of it only as about their relationship. Not even about the individual people, but about the relationship. Try to name the relationship (mentor/mentee? kindred spirits?) and see how it grows, what it becomes.
The RS Concern of Becoming (Changing One's Nature) almost certainly has to do with conflict around what the relationship is becoming, how the relationship is changing. And their relationship faces conflict from responsibility -- likely their responsibilities as incarnates but also, and most importantly for the RS, their responsibility to each other.
This story seems great! Though nothing in the storyform is ever written in stone, I like the Issues you have now -- I was secretly hoping you'd pick RS Responsibility, for example. That leaves you with OS Issue of Morality, which I like even better than Self-Interest because of how the characters are positioned around Ragnarok: they all think they're doing "what's best for the world". At least that was the sense I got.