We essentially agree on everything. Especially the autotrophic organelles working as a primary energy source(whether that’s ATP or something else to simplify the implementation). As for carbohydrate storage: you could have specialized “vesicles” that can store the different carbohydrates for now just by modifying the vesicle when you add it to your organism. Kinda like how lysozyme works rn.
I think that there is a way to stop the cycle without pyruvate, and the only reason I’m trying to make a decent argument for this is because it would be a much easier step in the right direction. If it works then the later addition of pyruvate and NADH might make the whole system even better and more stable. But showing these diagrams to non-biologists/biochemists is kinda overwhelming, and I think just difficult to code to start out with (I’ve had to code systems like this before for courses and they quickly turn into a nightmare). Gotta build a solid foundation both theory and programming-wise, then move up from there.
Here’s a new diagram showing an auto-inhibitory pathway for gluconeogenesis and glycolysis. I could be missing something though. Please point out any hole in this mechanism so that I can improve it! If I haven’t stopped the loop please explain how 
