Thanks for the feedback. The document model in mongo was slopped together by a junior engineer, so perhaps an unorthodox approach. It is basically flat, and already used in a pseudo-relational manner via in-app join to the existing sqlite store. This blog post inspired me to think, what if we just chucked all the json from mongo into sqlite and used the generated indices? Then we can gradually "strangler fig" endpoint by endpoint
That migration would be making two changes: document-based -> relational, and server -> library.
Have you considered migrating to Postgres instead? By using another DB server you won't need to change your application as much.