Inductive-coupling is yet another 3D integration technique that can be used to stack more than three known-good-dies in a SiP without wire connections. We present a topology-agnostic 3D CMP architecture using inductive-coupling that offers great flexibility in customizing the number of processor chips, SRAM chips, and DRAM chips in a SiP after chips have been fabricated. In this paper, first, we propose a routing protocol that exchanges the network information between all chips in a given SiP to establish efficient deadlock-free routing paths. Second, we propose its optimization technique that analyzes the application traffic patterns and selects different spanning tree roots so as to minimize the average hop counts and improve the application performance.