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Adapting small instruction-tuned models to specialized domains often relies on supervised fine-tuning (SFT) on curated instruction-response examples, which is expensive to collect at scale. Synthetic training examples generated by a teacher LLM from a domain corpus can reduce this cost, but existing pipelines can produce homogenized outputs and do not consistently capture cross-passage or cross-document dependencies. We introduce EmbGen, a synthetic data generation pipeline that decomposes a corpus into entity-description pairs, reassembles them using semantic structure inferred from embedding similarity, and then generates question-answer (QA) pairs via proximity, intra-cluster, and inter-cluster sampling with cluster-specialized system prompts. We evaluate EmbGen against EntiGraph, InstructLab and Knowledge-Instruct on three datasets of varied semantic heterogeneity, under fixed token budgets (5 and 20 million tokens). We use lexical overlap metrics, an LLM-as-a-judge rubric, and Binary Accuracy, a composed metric combining Factual Accuracy and Completeness for evaluation. EmbGen improves Binary Accuracy on the most heterogeneous dataset by 12.5% at 5M and 88.9% at 20M tokens budget, relative to the strongest baseline, while remaining competitive across other datasets with lower heterogeneity.