Incomplete multi-view clustering (IMVC) aims to exploit complementary information from multiple views with missing observations. Recent diffusion-based approaches have shown promise for view completion; however, they often fail to capture instance-aligned global correlations across views and suffer from inefficient inference and loosely coupled optimization. In this paper, we propose IASR, an Instance-Aligned Semantic Reconstruction framework for IMVC. IASR formulates missing-view recovery as a cross-view token alignment generator, in which noisy targets, observed views, and timestep embeddings are jointly represented as tokens and interact to capture long-range cross-view dependencies throughout the denoising trajectory. To stabilize representation learning under generative noise, we further introduce a stable–active dual-encoder representation architecture with a generative-adaptive contrastive learning strategy that tightly couples view completion and clustering. Extensive experiments on eight benchmark datasets demonstrate that IASR consistently outperforms state-of-the-art IMVC methods, especially under high missing-rate settings, while achieving improved inference efficiency.