4. Things would be way easier if the EE (and/or Frescobaldi) had a
method to highlight (colour-ing the grobs?) all mods, and a linking
method to navigate to the correct spot in the edition file. There was an
example of this [colouring part] some time ago, but I don't know if it
was "taken to the goal line"; it's worth looking at.
You are referring to overrides and such, right? Because objects inserted into the score via the EE do link properly (from what I've seen). This also "works" with mod lists, it is impractical however because the link is to the object, which is always at the start of the list, and then you have to navigate the list to find the proper moment. Not ideal but certainly better than nothing. However, it's for this reason that I was thinking about making a wrapper to make input with individual commands more convenient.
By the way, working with code such as your Mary Had a Little Lamb has to be a nightmare.