Large-scale multi-FPGA systems are widely used in modern emulation systems. As a critical part of the multi-FPGA system design flow, TDM signal grouping and package pin assignment directly impact the final placement and routing in the FPGA physical implementation. Poor pin assignments cause severe congestion and timing degradation at the logic-element level, while existing approaches lack accurate congestion modeling during system-level partitioning. This paper presents Chimew, a novel pin assignment methodology that leverages placement prototyping to predict logic-element-level congestion before physical implementation precisely. The proposed method co-optimizes signal grouping and pin placement through iterative refinement guided by congestion-aware cost functions derived from fast global placement. Experimental results demonstrate a 28% congestion reduction and up to 2.87ns less worst negative slack (WNS) compared to industrial tools while achieving a 100% success rate across diverse multi-FPGA benchmarks.