This is a very cool project! I'd actually considered doing something similar with my world as it would have more or less fit with the concept I'm working with, but ultimately I ended up building a new world from scratch. One thing you might consider is that you can download sample data for GPlates that goes back 400Mya or so, meaning that with a bit of work you could simulate your alternate earth quite nicely. It would require fiddling around a fair amount with their .rot files but the nice thing is that you'd have lots of data ready to go rather than having to start from scratch. Either way, excited to see how this progresses!