This published paper describes how Institute of Computing Technology (ICT), Chinese Academy of Science used S2C Dual Virtex-5 TAI Logic Modules to prototype a 100 million transistor-scale processor at 25MHz to boot unmodified operating system for carrying out a variety of architectural explorations. The paper identified several key challenges when prototyping a complex design onto multiple FPGA devices and how the ICT research engineers were able to solve these challenges including FPGA partitioning, pin limitations, emulating high-speed IO and debugging the design on S2C's TAI Logic Module.