AI accountability failures occur when regulatory audits examine outputs while root causes exist in instruction layers that remain undocumented and unauditable. Analysis of documented AI incidents including Air Canada's chatbot liability (2024), Amazon's hiring bias (2018), and Zillow's algorithmic valuation loss exceeding $500 million (2021) reveals a consistent pattern: problematic behavior traces to design-layer decisions involving objective functions, framework configurations, and data selection that were never systematically reviewed before deployment. Current AI governance frameworks including the EU AI Act, NIST AI Risk Management Framework, and ISO/IEC 42001 focus primarily on model outputs and data governance without providing technical specifications for documenting the full instruction stack from hardware substrate to emergent behavior. This creates a fundamental traceability gap where organizations can achieve nominal regulatory compliance while leaving the majority of their instruction stack unaudited. This paper introduces the Instruction Stack Audit Framework (ISAF), a proposed methodology designed to address this documentation gap. ISAF provides a nine-layer technical specification defining instruction propagation from voltage thresholds through objective functions to outputs, accompanied by a 127-checkpoint audit protocol for systematic instruction verification, an instruction lineage logging schema enabling cryptographic verification, a layer ownership assignment methodology for accountability attribution, and a risk scoring system based on abstraction distance and control strength. The framework draws on principles established in prior work on deterministic compliance systems and extends them to full-stack AI accountability. Three case analyses demonstrate how ISAF-based audits could have identified instruction-level risks in documented failures. The complete audit specification, logging schemas, and implementation templates are provided in appendices. ISAF is released for academic validation, industry pilot implementations, and regulatory consideration. Keywords: AI governance, algorithmic accountability, EU AI Act compliance, NIST AI RMF, ISO 42001, objective function auditing, instruction traceability, deterministic compliance, ML operations, AI safety, cryptographic audit trails, regulatory documentation requirements