It sounds like a really cool writing project!
If I understand correctly, you need to (1) organize the information and relate things in certain ways. (2) You also need to organize your book into chapters that you’re writing in Scrivener.
Regarding (1), if I were doing a project like this, I might instead use Obsidian to organize the recipes and other information and relate it to the generations and, of course, to your dad. Obsidian, even without the use of community plugins, natively lets you view connections.
Regarding (2), I might use AT and Scrivener (synced) strictly for the narrative writing, taking advantage of the timeline function of AT to track the dates of everything.
I’m just thinking out loud in case it is helpful. 