Am glad it's working for you.

The script below addresses #1 and #3. Am unclear about #2. Where is that newline appearing? Here's the script:

#!/usr/bin/perl
#
use strict;
use warnings;

$ARGV[0] or die "Usage: $0 <filename> [<filename>] ...";

my ( $template_file_name, $templateText, %hash ) = '';

for my $csvFile (@ARGV) {
    print "\nProcesing file $csvFile ...\n";
    open my $csvfh, '<', $csvFile or die "Unable to open $csvFile: $!"
+;

    # Ignore column names in first line
    my $columnNames = <$csvfh>;

    # Get vars from second line
    chomp( my $vars = <$csvfh> );
    my @vars = split /,/, $vars;

    while (<$csvfh>) {
        chomp;
        my @fields     = split /,/;
        my $templateFN = pop @fields;

        if ( $template_file_name ne $templateFN ) {
            $template_file_name = $templateFN;
            undef $templateText;
        }

        @hash{@vars} = @fields;

        $templateText //= getTemplateText($template_file_name);
        my $templateTextCopy = $templateText;

        $templateTextCopy =~ s/$_/$hash{$_}/g for keys %hash;

        my $ofile_name = $hash{'##rtrname##'} . '.txt';

        print "Writing to file: $ofile_name\n";
        open my $fh, '>', $ofile_name or die "$ofile_name: $!";
        print $fh $templateTextCopy;
        close $fh;
    }

    close $csvfh;
}

print "\nDone!\n";

sub getTemplateText {
    my ($template_file_name) = @_;

    local $/;
    open my $fh, '<', $template_file_name or die "$template_file_name:
+ $!";
    $templateText = <$fh>;
    close $fh;

    return $templateText;
}
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