This article presents a fully integrated 12-channel multiplexer with TE011 mode channel filters enabled by the unified extracted pole technique. A novel synthesis procedure is proposed to remove the limitation (a very small coupling) in the prototype with the classical approach. In addition, this article proposes a novel approach to assign the junction susceptance by simply shifting the length of the connecting waveguide section of the dangling resonators. The design process is then extended to the singly terminated case as the channel filter design. This work also proposes a novel analytical approach to derive the initial connecting phase lengths for the manifold multiplexer design. The circuit level optimization and space-mapping procedure for deriving physical dimensions are illustrated. The multiplexer is designed and constructed using a new clamshell structure, which offers low cost, small footprint, easy fabrication, and superior thermal performance. The simulated and measured results demonstrated that the proposed theory offers an excellent solution to the high-power waveguide manifold multiplexer designs.