I've built exactly one SOF kayak (from the Cunningham book) so you can take these thoughts with as large a grain of salt as you choose-

First, this sounds like an awesome project. You're both going to learn a lot.
As for "thinking ahead" with measurements- I followed the base design specs to a t. After paddling a few times, there were already things I wanted to do differently to another time- none of which I had predicted. Compared to a strip build, I found a SOF to be lightening fast and very affordable, so building a second, third, or tenth is totally plausible. I'd advocate for sticking with the design specs this first go round. It's so nice having a kayak designed around YOUR (current!) body, and it'll be a good baseline for future tweaks. AND she can probably build future kayaks solo!

Anyway, you didn't ask to be talked out of it ;)
So- I think part of the confusion might be caused by trying to work back from a chosen (essentially arbitrary) length. The book starts with paddler measurements to achieve overall length and beam placement, not the other way 'round. I'm thinking back to taking all of those measurements on a balance board- seems like you'd end up fudging a lot of those if you were only working off of an overall length measurement. Do you have access to an older sibling with a bit more height/weight on them that could serve as a stand-in for your future daughter?
Final thought- I'd venture that masik placement is the biggest potential gotcha in your circumstance. If the masik were positioned a bit higher on my thighs (as in- designed for a shorter person) I can imagine I'd still feel relatively stable and secure. Having it lower (designed for a taller person, as you plan) and having it hit my kneecaps or shins sounds pretty miserable. But that's a guess. Unfortunately, I'm also going to guess that it might be difficult to find SOF paddlers who didn't build to their own measurements that you can ask!
Good luck. Post pictures. Have fun. I'm sure it'll be great.

Patrick