Understanding fine-grained links between documents is crucial for many applications, yet progress is limited by the lack of efficient methods for data curation. To address this limitation, we introduce a domain-agnostic framework for bootstrapping sentence-level cross-document links from scratch. Our approach (1) generates and validates semi-synthetic datasets of linked documents, (2) uses these datasets to benchmark and shortlist the best-performing linking approaches, and (3) applies the shortlisted methods in large-scale human-in-the-loop annotation of natural text pairs. We apply the framework in two distinct domains -- peer review and news -- and show that combining retrieval models with LLMs achieves a 73% human approval rate for suggested links, more than doubling the acceptance of strong retrievers alone. Our framework allows users to produce novel datasets that enable systematic study of cross-document understanding, supporting downstream tasks such as media framing analysis and peer review assessment. All code, data, and annotation protocols are released to facilitate future research.