$text =~ s![#$%&~_}{^]!\\$&!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&~_}{^])
(?^:[#\$%&~_}{^])
[download]

Another way to completely defeat scalar or array interpolation in regexes (as in strings) is by use of  ' (single-quote) delimiters for the  s/// substitution:

c:\@Work\Perl\monks\marek1703>perl -wMstrict -le
"my $s = '-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0';
 print qq{'$s'};
 ;;
 $s =~ s' (?= [#$%&~_{}^]) '\\'xmsg;
 print qq{'$s'};
"
'-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0'
'-\#-\$-\%-\&-\~-\_-\}-\{-\^-0-\$\%\&\~\_\}\{\^0'
[download]

(This applies also to  m// and  qr// operators.) See perlop.

Interesting, I did not know that.

Sorry! One strange thing is happening: I get this:
1\0:\0\0
all "0" are escaped.

... all "0" are escaped.

That's because '0' (zero) is part of the character class: the value of  $% happens to be 0 at that point | the moment of regex compilation. Please see my update to the above.

Update: E.g.:

c:\@Work\Perl\monks\marek1703>perl -wMstrict -le
"my $s = '-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0';
 print qq{'$s'};
 ;;
 $s =~ s{ ([#\$%&~_{}^]) }{\\$1}xmsg;
 print qq{'$s'};
"
'-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0'
'-\#-\$-\%-\&-\~-\_-\}-\{-\^-0-\$\%\&\~\_\}\{\^0'
[download]

and also (no capture):

c:\@Work\Perl\monks\marek1703>perl -wMstrict -le
"my $s = '-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0';
 print qq{'$s'};
 ;;
 $s =~ s{ (?= [#\$%&~_{}^]) }{\\}xmsg;
 print qq{'$s'};
"
'-#-$-%-&-~-_-}-{-^-0-$%&~_}{^0'
'-\#-\$-\%-\&-\~-\_-\}-\{-\^-0-\$\%\&\~\_\}\{\^0'
[download]