There is little (unless these files are huge) need to make this so complicated. Just create the structure of the file in a AoAoA and process. No need to worry about multiple file handles, just use one over and over again. Whenever I tackle something like this, I almost always create the data structure and then process.

If you're having a tough time coming up with a solution, it's almost always a good idea to visulize/write down the data structure. Then the program makes itself. Oh and Data::Dumper is your friend.

use strict;
use warnings;

my @file = (
'1    2    3    4',
'5    6    7    8',
'9    10    11    12',
'13    14    15    16');

my @data;
foreach my $line (@file) {
    my @fields = split(/\t/,$line);
    for (my $x = 1 ; $x <= $#fields ; $x++) {
        push @{$data[$x-1]},  [$fields[0],$fields[$x]];
    }
    
}

for ( my $x = 0 ; $x <= $#data; $x++) {
    open(FH,">OUTPUT_$x") or die "$!\n";
    foreach my $fields ( @{$data[$x]} ) {
        print FH "$fields->[0] $fields->[1]\n";
    }
    close FH;
}
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