$text =~ s![#$%&~_}{^]!\\$&!g;

But only one character is not escaped: "%"

The sequence  $% is interpreted as the Perl special variable  $% (see perlvar) and its current value is interpolated. Try  [#\$%&~_}{^] (escaping the  $ character) instead.

Update: E.g.:

c:\@Work\Perl\monks\marek1703>perl -wMstrict -le
"my $sans_esc = qr/[#$%&~_}{^]/;
 print $sans_esc;
 ;;
 my $with_esc = qr/[#\$%&~_}{^]/;
 print $with_esc;
"
(?^:[#0&~_}{^])
(?^:[#\$%&~_}{^])
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