Background: The manuscript Yogasamuccaya, a late medieval Sangraha Grantha by Ganapativyasa, was authenticated through Critical Edition. The two paper manuscripts under study, offer invaluable physical evidences about the decorative elements, regional orthography, regional scribes, etc. Objective: The article focuses intensely on the Lower Criticism, aiming to provide a complete codicological description, document scribal errors and distinct orthographic conventions, and highlight the professional and cultural context of the copyists, thereby establishing a rigorous textual foundation for the newly edited text. Methodology: Side-by-side analysis of the two Devanāgarī paper manuscripts was performed for: physical dimensions, pagination, decorative elements, and scribal correction techniques. This quantitative documentation included 35 Scribal Errors and 81 Orthographic Peculiarities. Results: The manuscripts demonstrate a Gujrati scribal tradition. The copyist of Dn2 manuscript is identified in the end colophon as Raval Jaṭāśaṅkara Harajīvana, explicitly fulfilling the role of a Pustaka Lekhaka. Dn1 showcases a distinct, formal aesthetic, featuring unique diamond-shaped central gaps for floral drawings on the early folios and meticulously drawn triple-line margins in red ink. Philologically, the frequent and consistent confusion among the three Sanskrit sibilants (Śa, Ṣa, Sa) across both copies is a strong indicator of a shared regional linguistic habit within the transmission chain. Conclusion: The physical data and minute scribal habits of the Yogasamuccaya manuscripts are as important as the medical content. They validate the text's authenticity, anchor it to a specific regional and chronological context, and offer valuable materia critica for future comparative studies of Sanskrit medical codicology.