If I modify a core lua file how do I remake the format file? Is this
something that is done from mtxrun.exe? I would certainly prefer to use a
hook rather than modifying a core file, but how do I identify the hooks that
are available? Is there a list of hooks that are available, or a standard
way that hooks are called from the context code so that I can look for an
appropriate hook? Where do I place my hook scripts? Is there a guide that is
available that might get me started?

What I trying to do is map equation references to the equation number
generated by context. So for example, if I have an equation:

\placeformula \startformula
\NC F = m a \NC  \NR[eq:newtonslaw]
\stopformula