Its easier to focus on each problem if you name each problem :) ... argument passing is how to do subroutines

readFile( 'Text1', \@array1, \@data1 );
readFile( 'Text1', \@array2, \@data2 );
compareTheseThings( \@array1, \@data1 , \@array2, \@data2 );

sub readFile {
   my( $filename, $arrayref, $dataref ) = @_;
   use autodie qw/ open close /;
   open my($fh), '<', $filename ;
   ...
   push @$arrayref, ...;
   push @$dataref, ...; 
   ...
   close $fh;
   return;
}
[download]

use Data::Dump qw/ dd /;
## this?
{
    my( %RedText, %DerText );
    $RedText{'Entry 1'}{D}=1;
    $RedText{'Entry 1'}{N}=2;

    $DerText{'Entry 3'}{N}=6;
    $DerText{'Entry 3'}{""}=7; ## uh oh, something fishy
    
    $DerText{'Entry 5'}{D}=4; ## uh oh, duplicates overwrite, no good
    $DerText{'Entry 5'}{D}=9;
    
    dd( \%RedText, \%DerText );
}

## maybe this?
{
    my( %RedText, %DerText );
    
    $RedText{'Entry 1'}{1}='D';
    $RedText{'Entry 1'}{2}='N';

    $DerText{'Entry 3'}{6}='N';
    $DerText{'Entry 3'}{7}='';
    
    $DerText{'Entry 5'}{4}='D';
    $DerText{'Entry 5'}{9}='D';
    
    dd( \%RedText, \%DerText );
}
[download]

"entry_id", "fist_number", "second_letter"
$hash{"entry_id"}{"fist_number"} = "second_letter";
$bothfiles{first_file}{"entry_id"}{"fist_number"} = "second_letter";
[download]

does this make sense to you?