Sounds like a great plan! When I read Yotsuba, all I did was make notes on the pages themselves. Now I do a lot more of what you’re doing, and it is working very well for me.
I’ve never used Anki but I do use Kitsun. I was using the N5 deck and 10K vocab deck only, but have recently discovered that making your own decks is not so hard and I’m having a lot of fun with it.
Good luck and don’t forget to read through the Yotsuba threads here! Pretty much any questions you have will have been answered, but if you find any more, please ask!