Modelling is hard

It's hard without a quantum computer. That is also hard, but in a different way. Anyone know about how likely it is that we'll ever have quantum computers that are good enough for this?

Chaos

The issue isn't trying to control it in the face of chaos. It's to make the system stable, or at least make sure the attractor is small enough that it is, for all intents and purposes, stable. You have to eliminate all the degrees of freedom, or at least all the ones that actually matter. You might not care where your factory went off to so long as it keeps running.

4a. False. Flexible diamond doesn't make any sense.

Pretend that they said carbon nanotubes, and that they described the construction of carbon nanotubes instead of diamond.

What set of instructions can a collection of 50 carbon atoms accept and execute? How are these instructions being delivered?

Either you make it a lot bigger than 50 carbon atoms and just make that the size of whatever is actually moving things, or you don't bother with making it programmable, and you just send the instructions as needed.

As for how you could make a computer that small, running a Turing machine with a DNA molecule as the tape comes to mind. It's much bigger than 50 carbon atoms, but you could still make the actual factory part that small, so long as you don't mind it moving around as it computes. There's likely a better computer design. I don't really know much about this stuff.

If you can move individual atoms around, you can build an atomic computer that computes by moving individual atoms around.