Physical neural networks (PNNs) exploit diverse physical substrates---spanning molecular, wetware, and solid-state devices---to perform embodied neural computation close to physical processes. However, their operational heterogeneity in signal modalities, timing regimes, reset requirements, calibration lifecycles, and observability prevents their integration as interchangeable execution endpoints in edge, fog, and cloud workflows. We present CP$^2$N$^2$, a substrate-aware control-plane architecture that bridges software-level orchestration and physical neural computing. CP$^2$N$^2$ introduces a three-plane model that decouples high-level orchestration, twin-state synchronisation, and substrate-specific execution under versioned Physical Neural Resource Contracts. It extends Model Context Protocol (MCP)-style discovery and invocation with explicit lifecycle management, atomic leases, telemetry freshness verification, and fail-closed safety boundaries. We evaluate a reference prototype across contrasting behavioural twins, a same-host multi-process deployment under fault injection, and the Cortical Labs SDK Simulator. In a 945-request concurrency campaign, CP$^2$N$^2$ enforces typed contention and fail-closed recovery with sub-millisecond local orchestration overhead. Furthermore, in a 160-decision Agent-to-PNN campaign with a hosted LLM planner, independent enforcement ensured that 100% of executed actions remained strictly safe, verified, and reconciled despite planner-level inconsistencies. CP$^2$N$^2$ thus provides an enforceable systems abstraction for integrating scarce, stateful physical AI substrates into agentic computing environments.

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