@CaseyMiller the individual issues for your article appear to be:

1. latexml needs new support for orcidlink.sty - this is also a common request in arXiv/ar5iv

2. The \hrule bug could be worth distilling into a minimal example and submitting as a separate issue, could be schema-related

3. Footnotes appear to use a custom technique, likely also warranting its own issue:

   % Unnumbered footnotes
   \newcommand\blfootnote[1]{%
     \begingroup
     \renewcommand\thefootnote{}\footnote{#1}%
     \addtocounter{footnote}{-1}%
     \endgroup
   }

4. Affiliations are realized via authblk.sty and this may be a binding support regression - we'd need to investigate. That could also be turned into a separate issue with a minimal example where the affiliations disappear.

Thank you for the report! These are valuable to detect and patch.

• latexml needs new support for orcidlink.sty - this is also a common request in arXiv/ar5iv

Quick note: orcidlink.sty can almost be read raw. What's missing is the \fontcharht primitive, which is used to determine the size of the logo, and that does not seem very easy to implement (LaTeXML knows few font metrics).