Thin films of crystalline solids with substantial free volume built from organic chromophores and metal secondary building units (SBUs) are promising for engineering new optoelectronic properties through control of interchromophore coupling. Zn-based SBUs are especially relevant in this case because they avoid quenching the chromophore's luminescence. We find that layer-by-layer spin-coating using Zn acetate dihydrate and benzene-1,4-dicarboxylic acid (H2BDC) and biphenyl-4,4'-dicarboxylic acid (H2BPDC) linkers readily produces crystalline thin films. However, analysis of the grazing-incidence wide-angle X-ray scattering (GIWAXS) data reveals the structures of these films vary significantly with the linker, and with the metal-to-linker molar ratio used for fabrication. Under equimolar conditions, H2BPDC creates a type of structure like that proposed for SURMOF-2, whereas H2BDC generates a different metal-hydroxide-organic framework. Large excess of Zn2+ ions causes the growth of layered zinc hydroxides, irrespective of the linker used. Density functional theory (DFT) calculations provide structural models with minimum total energy that are consistent with the experimentally observed diffractograms. In the broader sense, this work illustrates the importance in this field of careful structure determination, e. g., by utilizing GIWAXS and DFT simulations to determine the structure of the obtained crystalline metal-organic thin films, such that properties can be rationally engineered and explained.