After reading the MathJax documentation a second time, I figured out how to use MathJax to achieve the cross referencing and equation numbering:

= Test eqn cross-ref
:stem: latexmath
:eqnums:
== Let's try
\begin{equation}\label{myequation}
c^2 = a^2 + b^2 + 5
\end{equation}
I refer back to \eqref{myequation}.

This will work well for what I need at the moment.