-How will the genome of cells be represented?
-How will the genomes express themselves?
-What mutation functions will be used?
All these questions above are critical to the core of your alife program and should be addressed as soon as you have decided what your world will be, which you have.
The issues of genome representation and expression are the *most problematic* in evoluting alife worlds. If you don't get them right or make them too "simple" then evolution will not happen. Good examples of this are a number of my failed projects!
I attempted ambitious projects like this when i first got into alife and they all failed due to the genome representation and expression. I friendlily suggest you attempt a small simulation of this sytem first with a small 2D world before you move it into such a colossal 3D universe. The principles of your genetic model should be able to operate in 2D and 3D and small and large universe alike. Get this working in small 2D and it will work in big 3D. Basically get the genetic algorithm working first is my suggestion.
Currently I am now working on a relatively simple alife project to do with evolving structures of 2D plants (which don't move so it's easier
I will watch eagrely on this topic and wish you the best of luck. Don't worry if this project runs out of steam, lots of mine have and I just pick myself up, learn from its problems and try a new one.