Despite the fact that there is an existing body of literature addressing the computation of Coupling Loss Factors (CLFs) via the Finite Element Method (FEM), no publications have sufficiently taken into account real structural joints in their approach. Previous research has focused on academic cases of trivial connections, rarely involving more than two steel plates. To enable Statistical Energy Analysis (SEA) on a real ship, a methodology for determining CLFs for non-trivial systems is proposed, considering realistic boundary conditions and irregularities that can occur in marine structures. Based on the method, a library of CLFs is created by selecting the tested connections to enable modelling of about 90% of the acoustic paths on an existing jack-up vessel. Boundary conditions were set by introducing spring elements with a stiffness calibrated to the type of connection and taking the adjacent structure into account. In previous works, CLFs were determined for basic connections of rectangular plates. The lack of scantling variations, ignoring discontinuities and only defining parallel edges in the considered models, lead to the overestimation of energy transmission in real structures. To consider the influence of the above, random deviations from the initial stiffness of the springs at individual edges and point restraints at random points are introduced in this paper.