The interstellar medium of the Milky Way represents a complex coupling of various constituents, where transport and interactions of cosmic rays (CRs) play a major role. They are further influenced by the spatial distribution of CR sources, Galactic gas, starlight, and magnetic fields. As part of a series of Galactic 3D reconstructions, we solve the CR transport problem through the numerical framework PICARD. Here, we introduce 3-dimensional gas distributions for the atomic (HI) and molecular (H2) components; reconstructed from direct spectral line measurements for the former, and CO surveys for the latter. These results are studied independently from the standard approach, where the Galactic structures are determined by so called ring models. In this study, CR source distributions are introduced in the simulations as axially symmetric models. As a result, all Galactic structures are defined entirely by the gas reconstructions. Furthermore, the results of CR distributions are used to study gamma-emission, in particular the pion decay and bremsstrahlung components. We compare said components with results obtained by use of the High-Energy Radiative Messengers (HERMES) framework. This shows the difference between the ring and 3-dimensional modeling approaches, where the lack of near-far ambiguity in the latter is of main interest and presents the main advantage of transitioning towards 3-dimensional maps of transport relevant quantities.