After corresponding with JM, determined list of priorities for the conversion. I decided to do H5 first since it is one of the most densely annotated/collated and the editorial process should be swift.
Converted H5_FM and Q1M and got annotations working; there were a few bugs in the HTML code, which I fixed. Also discovered the issue with part lines; the IML usually flagged the part lines with an empty line preceding the inferred line (i.e. via one of the LNs), so re-wrote bits of the conversion to handle that. Also had to make various fixes to the apparatus linking code to handle supplied tags.