hey mate
is this what you need?

use Inline::Files;
%h = qw/and nand or xor/;

$f = sub {
    $fh = shift;
    while(<$fh>){
        chomp;
        $m = $_ and $a{$m} = {} and next if /^module/;
        $l = \@{$a{$m}{'in'}} if /^input/;
        $l = \@{$a{$m}{'out'}} if /^output/;
        $l = \@{$a{$m}{'op'}} and ($_ = $_) =~s/$&/$h{$&}/ if /^and|^o
+r/;
        $l = \@{$a{$m}{'cond'}{$_}} if /^if/;
        next if /endmodule/;
    push @{$l}, $_;
    }
    return %a;
};

%r = &$f(FILE1);
%s = &$f(FILE2);

for( keys %r){
    print "\n\n$_\n";
    print "@{$r{$_}{'in'}}\n";
    print "@{$r{$_}{'out'}}\n";
    print "$r{$_}{'op'}[0]";
        for $x (keys %{$r{$_}{'cond'}}){
            if(defined $s{$_}{'cond'}{$x}){
                print "\n",join"\n",@{$s{$_}{'cond'}{$x}};
            } else {
                print "\n",join"\n",@{$r{$_}{'cond'}{$x}};
            }
        }
    print "\nendmodule\n";
}



__FILE1__
module and_1 (y,a,b);
input a, b;
output y;
and x1 (y,a,b);
if ( a == b)
y = 1'b0;
else
y = 1'bx;
if ( a == 1 )
y = 1'b1;
else
y = 1'b0;
endmodule
module or_1 (y,a,b);
input a, b;
output y;
or x1 (y,a,b);
if ( a == b)
y = 1'b0;
else
y = 1'bx;
if ( a == 0 )
y = 1'b0;
else
y = 1'b1;
endmodule
__FILE2__
module and_1 (y,a,b);
input a, b;
output y;
and x1 (y,a,b);
if ( a == b)
y = 1'bx;
else
y = 1'b0;
if ( a == 0 )
y = 1'bx;
else
y = 1'b1;
endmodule
module or_1 (y,a,b);
input a, b;
output y;
or x1 (y,a,b);
if ( a == b)
y = 1'b1;
else
y = 1'b0;
if ( a == 0 )
y = 1'bz;
else
y = 1'bx;
endmodule
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