I had thought about removing versus just disabling, but not displacing nodes. Highlighting changes would keep the referential position of other options present, but visually enhance the method. Perhaps being able to drag nodes (locked to a grid even) to make paths easier to trace. Visual adjustments of path thickness, color based on simple parameters, etc. There is a ton you can do.
The second idea was kind of looking at later useful complexities and half at simple math inclusions where each step hierarchically references what material numbers are needed. Just a simple number representation of the ratios of production, time notwithstanding, is a useful piece.
Perhaps displayed by the ingredient lines when zooming in a format like this: This-step (aggregate-steps)
Exactly what I have in mind is proving difficult to quantify at the moment, but you are off to a fascinating start.
Another idea might be having an option to pause the game while in the Dana interface, similar to research. I know you are just starting, so there is a lot of ground yet before I expect you have this rough proof developing into a refined tool.
But do take care with the balance of things you add. The best place to land is somewhere between Microsoft bloat and oversimplified Apple. Both have issues, but a default setting of minimalism with nearly dev-grade options to enable for those that want to nerd out will likely give you plenty of room.
Factorio is remarkably simple in its core aspects, but the interactions of all the simple parts coming together are what keeps us engaged.
Edit: I know very small amounts of programming, but it seems reasonable to set a flag on every entry (side menu to open?) that can be unchecked and manually remove it from the query.