This is a sequel to the second and third author's Mixed Dimer Configuration Model in Type $D$ Cluster Algebras where we extend our model to work for quivers that contain oriented cycles. Namely, we extend a combinatorial model for $F$-polynomials for type $D_n$ using dimer and double dimer configurations. In particular, we give a graph theoretic recipe that describes which monomials appear in such $F$-polynomials, as well as a graph theoretic way to determine the coefficients of each of these monomials. To prove this formula, we provide an explicit bijection between mixed dimer configurations and dimension vectors of submodules of an indecomposable Jacobian algebra module.