How do I best get it to take everything following the header:

<$fh_in>;  # Skip header
print $fh_out $_ while <$fh_in>;
[download]

Or if you don't mind loading the entire input file into memory:

<$fh_in>;  # Skip header
{ local $/; print { $fh_out } <$fh_in>; }
[download]

By the way, '.' indicates the current directory, so there's no need to load Cwd.

By the way, $_ != /\.ktf$/ makes no sense. You probably meant $_ !~ /\.ktf$/ (long for !/\.ktf$/). But isn't that inverted? I think you want /\.ktf$/ (short for $_ =~ /\.ktf$/).

So you get:

use strict;
use warnings;

use File::Find qw( find )

open(my $fh_out, '>', 'D:\\mergedfile.ktf')
    or die("Can't create output file \"D:\\mergedfile.ktf\": $!\n");

my $first = 1;

find(sub {
    return if !/\.ktf\z/;

    print("$File::Find::name\n");
    open(my $fh_in, '<', $File::Find::name)
        or die("Can't open file \"$File::Find::name\": $!\n");

    <$fh_in> if !$first;
    $first = 0;

    print $fh_out $_ while <$fh_in>;
}, '.');
[download]

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