One of the things that I came across when writing my own janky pdf/latex->html converter for lecture notes[0] is that Pandoc doesn't handle references and subfigures correctly, even with pandoc-crossref and pandoc-citeproc enabled. I had to write a little python module[1] that used regex to extract those and then handle them on my own separately... This is definitely something you should look at.

[0] https://dmaitre.phyip3.dur.ac.uk/NPP/notes/ [1] https://github.com/JBorrow/latex-pandoc-preprocessor