I am guessing I still don't have this correct because the plots do not match. If you can find any mistakes that I have made then please point them out. I'm trying to reproduce your very first example.
If you can think of any little experiment we can try on simpler made-up systems then maybe that would confirm that simpler examples do match between Excel and Mathematica.
If I look at the equations for each row of your Excel sheet then I think I see
t+dt,((BX*MX/(1+KZ*zm)-xm/TX)*dt+xm)/dt,((BY*MY/(1+KX*xm)-ym/TY)*dt+ym)/dt,((BY*MY/(1+KX*ym)-zm/TY)*dt+zm)/dt
I think that is what I am trying to reproduce in Mathematica, with the translation from discrete to differential equation. But it still seems like I am misunderstanding something.
