In this paper we present our work-in-progress on a fully-implemented pipeline to create deeply-annotated corpora of a number of historical and contemporary Tibetan and Newar varieties. Our off-the-shelf tools allow researchers to create corpora with five different layers of annotation, ranging from morphosyntactic to information-structural annotation. We build on and optimise existing tools (in line with FAIR principles), as well as develop new ones, and show how they can be adapted to other Tibetan and Newar languages, most notably modern endangered languages that are both extremely low-resourced and under-researched.