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Porous, stacked two-dimensional covalent organic frameworks (2D COFs) bearing semiconducting linkers can support directional charge transfer across adjacent layers of the COF. To better inform the current and possible future design rules for enhancing electron and hole transport in such materials, an understanding of how linker selection and functionalization affects interlayer electronic couplings is essential. We report electronic structure simulation and analysis of electronic couplings across adjacent linker units and to encapsulated species in functionalized electroactive 2D COFs. The detailed dependence of these electronic couplings on interlayer interactions is examined through scans along key interlayer degrees of freedom and through configurational sampling from equilibrium molecular dynamics on semiempirical potential energy surfaces. Beyond affirming the sensitivity of the electronic coupling to interlayer distance and orientation, these studies offer guidance toward linker functionalization strategies for enhancing charge carrier transport in electroactive 2D COFs.