Hermaphrodites in New Granada (around 1800)
Once you start looking … you find them everywhere: in addition to hermaphrodites in Florida, Mexico, Guatemala, there are several published reports on hermaphrodites in (Spanish) America. For example, Vazquez Garcia / Cleminson 2013, 158 n. 60 list a few of them. An online article they quote (Giraldo 2008) seems to have vanished in 2013 or so, but can be recovered thanks to archive.org: https://web.archive.org/web/20091217165949/http://www.incertidumbre.org/index.php?option=com_content&task=view&id=85&Itemid=55, and partly overlaps with another article by the same author (Giraldo 2010).
Without (for the time being) access to the primary sources quoted, I simply provide bibliographic details and links to materials available online. Strikingly, one case took place the very year Juana la larga was tried in Guatemala: in this year 1803, there also was another trial against an alleged hermaphrodite in the Viceroyalty of New Granada (this time, in modern Columbia):
Secondary literature quoted
Richard Cleminson / Francisco Vázquez García, Sex, Identity and Hermaphrodites in Iberia, 1500–1800, London 2013. https://books.google.de/books?id=g5FECgAAQBAJ
Carolina Giraldo, Sexualidades intermedias en la prensa colonial hispanoamericana: Tres estudios de caso, in: Tinkuy: Boletín de investigación y debate (2010), 119-138. https://dialnet.unirioja.es/descarga/articulo/3296429.pdf