Before seeing your code, I had tried something similar but limited only to $1. Now I've worked on it a bit more and came up with this. Just another WTDI.

use warnings;
use strict;

my $user_defined_string = "There's more than one way to do it (more th
+an one).";
my $user_defined_search = '(more)(.*?)(one)';
my $user_defined_replace = '<b>$1</b>$2<b>$3</b>';

my (@subs) = $user_defined_string =~ /$user_defined_search/;
for my $sub (1..@subs) {
  $user_defined_replace =~ s/\$$sub/$subs[$sub-1]/ge;
}

print "mangled replace: $user_defined_replace\n";
$user_defined_string =~ s/$user_defined_search/$user_defined_replace/g
+e;
print "after: $user_defined_string\n";

__OUTPUT__

mangled replace: <b>more</b> than <b>one</b>
after: There's <b>more</b> than <b>one</b> way to do it (<b>more</b> t
+han <b>one</b>).
[download]

As we can see, the user is expected to have a deep understanding of Perl regexes (non-greediness in this example) if she wants to do fancy stuff ;^).