... perl substitutions ... are kept as lists in separate files and are read in by a processing engine, which then essentially does this: eval $mySubstitution. We now need to keep track of what was matched and their positions in the document.

I think the approaches based on \G already posted will serve perfectly well. However, I cannot help thinking the original eval-based process (insofar as I understand it) could easily be extended.

I imagine the process described above as in the first code sequence below: regex strings and replacement strings wind up in an array or arrays; a loop works through the array(s) eval-ing a  s/// statement for each substitution.

This could easily be extended as in the second code sequence below. No change whatsoever to either regex string or replacement string seems necessary.

>perl -wMstrict -le
"my @search  = qw(foo fee fie  foe );
 my @replace = qw(bar fum \u$& \U$&);
 ;;
 my $document = 'the foo is fee and fie-foe.';
 ;;
 while (my ($i, $rx) = each @search) {
   eval qq{ \$document =~ s{$rx}{$replace[$i]}g };
   }
 print qq{'$document'};
 ;;
 $document = 'all foo are fee or fie/foe';
 ;;
 my @replaced;
 while (my ($i, $rx) = each @search) {
   eval qq{
     \$document =~
       s{$rx}
        { push \@replaced, [\$&,\$-[0],\$+[0]]; qq{$replace[$i]} }eg
     };
   }
 print qq{'$document'};
 use Data::Dumper;
 print Dumper \@replaced;
"
'the bar is fum and Fie-FOE.'
'all bar are fum or Fie/FOE'
$VAR1 = [
          [
            'foo',
            '4',
            '7'
          ],
          [
            'fee',
            '12',
            '15'
          ],
          [
            'fie',
            '19',
            '22'
          ],
          [
            'foe',
            '23',
            '26'
          ]
        ];
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