Alphabetic spelling systems rarely display perfectly consistent one-to-one relationships between graphic marks and speech sounds. This is particularly true for languages without a standard written form. Nevertheless, such non-standard spelling systems are far from being anarchic, as they take on a conventional structure resulting from shared communities and histories of practice. Elucidating said structure can be a substantial challenge for researchers presented with textual evidence alone, since attested variation may represent differences in sound structure as well as differences in the grapho-phonological mapping itself. In order to tease apart these factors, we present a tool — Medusa — that allows users to create visual representations of the relationship between sounds and spellings (sound substitution sets and spelling substitution sets). Our case study for the tool deals with a longstanding issue in the historical record of mediaeval Scots, where word-final ⟨cht⟩, ⟨ch⟩, ⟨tht⟩ and ⟨th⟩ appear to be interchangeable, despite representing reflexes of distinct pre-Scots sounds: [x], [xt] and [θ]. Focusing on the documentary record in the Linguistic Atlas of Older Scots (LAOS 2013), our exploration surveys key graphemic categories, mapping their lexical distributions and taking us through evidence from etymology, phonological typology, paleography and historical orthograpy. The result is a novel reconstruction of the underlying sound values for each one of the target items in the record, alongside a series of sound and spelling changes that account for the data.