We implement a general method for correcting the low-bias transport properties of nanoscale systems within an ab initio methodology based on linear combinations of atomic orbitals. This method consists of adjusting the molecular spectrum, i.e. shifting the position of the occupied and unoccupied molecular orbitals to match the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO (HL)) gap. Thus we show how the typical problem of an underestimated HL gap can be corrected, leading to quantitative and qualitative agreement with experiments. We show that an alternative method based on calculating the position of the relevant transport resonances and fitting them to Lorentzians can significantly underestimate the conductance and does not accurately reproduce the electron transmission coefficient between resonances. We compare this simple method in an ideal system of a benzene molecule coupled to featureless leads to more sophisticated approaches, such as GW, and find rather good agreement between both. We also present the results of a benzenedithiolate molecule between gold leads, where we study different coupling configurations for straight and tilted molecules, and show that this method yields the observed evolution of two-dimensional conductance histograms. We also explain the presence of low-conductance zones in such histograms by taking into account different coupling configurations.