Unless c1 etc. are regular expressions, you'll want to use quotemeta. Here's a simple version that does more or less what you want, I think:

my ($fa, $fb) = @ARGV;
open IN, $fa or die $!;
my %h;
while (<IN>) {
    my ($str, $rep) = (split)[2,3];
    $h{$str} = $rep;
}

my $pat = join '|', map { quotemeta $_ } keys %h;
$pat = qr/\b($pat)\b/;
print STDERR "$pat\n";

open IN, $fb or die $!;
while (<IN>) {
    s/$pat/$1$h{$1}/g;
    print;
}
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