Do you mean, "once a full description of the universe is in hand", and that the 10000 bits are the complexity of locating W1 and W2 in the full description?

Yes, and describing the procedures "read the voltage off W1 at the following sequence of times" and "set the voltage on W2 at the following sequence of times."

What might be the complexity of locating W2 conditional on having located W1? It seems plausible that this extra complexity would be within a constant of the complexity of describing the AIXI algorithm and something like counterfactual physical reasoning about alternative inputs, to check whether the known behavior of AIXI is consistent with W2 given counterfactual input at W1.

The conditional complexity seems substantially lower (you don't need to describe AIXI, I think, because you get its output for free?), but still large enough to make the argument go through.