Interesting that you went with the wendigo.... lol not a commonly used creature. However I do have one thing that you continue to talk about in the fic with Rares and Jack that I disagree with the way you'll go about it xD but that's me.

I always felt it made more sense for Rarity to be the birth mother of kids between the two of them. Especially with Jack being so masculine in this world and being a monster hunter lol buuuut that's just my opinion xP

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Normally I'd agree, but in this case it'd be far harder to do if they wanted a more "traditional" approach.
Soul-folk can physically alter their bodies with relative ease, including gender for a time, if you look at the first story. Altering someone else, however, would require a far stronger investment in magic, especially an earth-folk. It's something Twila could do for sure in order to help with their situation, but not Rarity, she doesn't really have the magical prowess. So, rather than relying on a third party, Rarity and Jack would probably choose the path of least resistance and the one that lets them rely on themselves more. Sure, you can also make the suggestion for a surrogate or someone donating sperm, but I see the two wanting to be as self-reliant on their own answers and solutions as possible due to their more independent streaks.