Because of the complexity of the operation, I am actually matching a chunk at a time (it is this step where I've run into the "false positives" problem and need a priority-match solution) and then I am substituting via an evaluated subroutine which processes the captured chunk and returns the correct replacement. So, in a sense, I am doing this already--but in stages, via the subroutine.

For the basic idea:

$str = s~[my regex]
~print "DEBUG: 3:$3; 4:$4; 5:$5; 6:$6\n"; $procfootnote->()~egmx;
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I'm no stranger to regex...but regex is sufficiently complex that I doubt I'll ever fully master it!