Coaxial waveguides are frequently used in order to feed and interconnect a wide variety of microwave and millimeter wave devices (filters, diplexers, multiplexers, etc.). As a consequence, the rigorous and efficient characterization of the coaxial excitacion of waveguide structures is a very important topic that has been widely studied in the technical literature. However, a few number of these contributions investigate this problem from a multimodal point of view. The main objective of this work is the efficient multimodal characterization of the coaxial excitation of waveguide components using the 3D BI-RME (Boundary Integral - Resonant Mode Expansion) method. In particular, two types of configurations widely used in practical applications are discussed: the classical coaxial excitation, and the coaxial excitation based on an end-launcher configuration. The end-launcher configuration is commonly used to feed comb-line filters, which are also investigated in this work. Concretely, a very efficient CAD tool for the analysis and design of comb-line filters has been developed. The analysis and design of compensated waveguide junctions using partial-height metallic posts is also a main objective of this investigation. Following the 3D BI-RME method, we present the design of a great variety of compensated waveguide junctions (right-angled bends, T junctions, magic T junctions, and turnstile junctions) with an optimum electrical performance. Moreover, we demonstrate that the relative position of the metallic post in the structure is a very important design parameter that has not been taken into account in previous works concerning compensated junctions using partial-height metallic posts.