Using the Evans spectral sequence and its counter-part for real $K$-theory, we compute both the real and complex $K$-theory of several infinite families of $C^*$-algebras based on higher-rank graphs of rank $3$ and $4$. The higher-rank graphs we consider arise from double-covers of cube complexes. By considering the real and complex $K$-theory together, we are able to carry these computations much further than might be possible considering complex $K$-theory alone. As these algebras are classified by $K$-theory, we are able to characterize the isomorphism classes of the graph algebras in terms of the combinatorial and number-theoretic properties of the construction ingredients.