Stable organic radicals integrated into molecular junctions represent a practical realization of the single-orbital Anderson impurity model. Motivated by recent experiments for perchlorotriphenylmethyl (PTM) molecules contacted to gold electrodes, we develop a method that combines density functional theory (DFT), quantum transport theory, numerical renormalization group (NRG) calculations and renormalized super-perturbation theory (rSPT) to compute both equilibrium and non-equilibrium properties of strongly correlated nanoscale systems at low temperatures effectively from first principles. We determine the possible atomic structures of the interfaces between the molecule and the electrodes, which allow us to estimate the Kondo temperature and the characteristic transport properties, which compare well with experiments. By using the non-equilibrium rSPT results we assess the range of validity of equilibrium DFT + NRG-based transmission calculations for the evaluation of the finite voltage conductance. The results demonstrate that our method can provide qualitative insights into the properties of molecular junctions when the molecule-metal contacts are amorphous or generally ill-defined, and that it can further give a fully quantitative description when the experimental contact structures are well characterized.