Universal channel decoders based on transformers-such as the Foundation Error Correction Code Transformer (FECCT)-achieve competitive decoding performance across diverse code families with a single shared backbone, optionally followed by code-specific finetuning. However, the high computational complexity and large parameter footprint of FECCT present substantial obstacles to practical deployment. To address these challenges, we investigate structured pruning for FECCT and propose Spectral-Aligned Pruning (SAP), a structure-aware framework that enables cross-code reuse of structured pruning masks by leveraging the spectrum of the corresponding bipartite graph. SAP is grounded in classical graph analysis of codes: the two algebraically largest adjacency eigenvalues provide compact spectral proxies for degree scale, expansion ratio, and minimum-distance lower bounds. These quantities are directly relevant to decoding performance: degree scale reflects how densely codeword bits and parity checks are connected; expansion ratio influences how information propagates across the bipartite graph; and minimum distance characterizes codeword separation. Based on this connection, SAP uses these two leading eigenvalues as a lightweight code signature for pruning-mask retrieval. Empirically, this two-dimensional signature yields stable library selection equivalent to higher-dimensional spectral signatures in our evaluation. After pruning, SAP uses parameter-efficient low-rank adaptation (LoRA) to recover decoding performance while storing only a small number of additional adapter parameters per code. Experiments across diverse codes show that SAP achieves decoding performance comparable to dedicated per-code pruning, while enabling substantial reductions in computational cost and model memory footprint through kernel-level structured pruning. Code is available at https://github.com/iil-postech/sap.

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