Current computational approaches---rigid-host Monte Carlo and one-dimensional classical density functional theory (cDFT)---cannot quantitatively predict cooperative pore filling, framework flexibility, or kinetic molecular sieving in nanoporous hosts. We present porecdft, a modular three-dimensional cDFT framework that combines an orientation-averaged composite external potential (Lennard--Jones + Gaussian-smeared Coulomb + quadrupole--electric-field-gradient), advanced White-Bear II fundamental measure theory with Wertheim first-order thermodynamic perturbation theory (TPT-1) site association, an elastic framework response, and an Anderson-accelerated solver. Demonstrated on the CO\(_2\)/aluminum-formate (ALF) benchmark of Evans et al. (Sci. Adv. 2022), the framework reproduces the periodic-DFT binding energies at both small (\(-48\) vs \(-48.4\)~kJ\,mol\(^{-1}\)) and large cavities within 1%, the 298~K isotherm with a root-mean-square error (RMSE) of 0.33~mmol\,g\(^{-1}\), and the experimental calorimetric isosteric-heat band (25--32~kJ\,mol\(^{-1}\)). The anomalous experimental temperature ordering \(N(323~\textrm{K}) \approx N(298~\textrm{K}) \gg N(273~\textrm{K})\) is identified as a kinetic effect of formate-linker librations directly observed in ab initio molecular dynamics, while the cDFT CO\(_2\)/N\(_2\) Ideal Adsorbed Solution Theory (IAST) selectivity of \(\sim\)4 lies two orders of magnitude below the experimental kinetic value of 350--600, confirming ALF as a kinetic molecular sieve whose selectivity arises from transport rather than equilibrium. As a second benchmark, the framework is applied to H\(_2\) adsorption in four metalated covalent organic frameworks (COF-301, COF-322, COF-330, COF-333) loaded with five first-row transition metals using Morse external potentials; cobalt gives the highest Henry-regime uptake in every COF owing to its broad, soft Morse well rather than its well depth, a result requiring 3D treatment to capture.