Text alignment is a process of locating similar passages across different versions of documents. The degree to which two passages are similar is a matter open to debate; what similarity means in literature may be mathematically undefinable, due to the non-logical structure of human language. Buddhist texts often occur in multiple versions for various reasons, including document drafts, sectarian disagreements, and other phenomena of text transmission. While some alignments between texts seem obvious to human readers, there are also instances where alignment boundaries are ambiguous or unresolvable even for trained specialists. Using a custom genetic algorithm, I demonstrate some ways that these ambiguities can be transformed from obstacles into assets in the analysis of unknown texts.