The reason they aren't compiling properly is that s/// is an operator. If you are going to be compiling regexps from a string, you need only compile the left-hand side of a s///, as the right-hand side is essentially a double quoted string.

use strict;

my $re  = qr/foo./;
my $str = "foo bar baz";

$str =~ s/$re/FOOD /;

print "$str\n";

__output__

FOOD bar baz
[download]

HTH

broquaint