If I understood correctly, you want something like:

• Read and parse the sequences file
• For each sequence, open a file that is named after the sequence header
• From that file, get the first number of each line
• Associate each letter in the sequence with those numbers

use strict;
use warnings;

my ($seqfile) = @ARGV;
#seqfile is the file with the sequences.

open my $seqfh, "<", $seqfile or die $!;

{
  local $/ = "\n>";
  while (my $nextseq = <$seqfh>){
    chop $nextseq unless eof $seqfh;
    substr ($nextseq,0,1,"") if $. == 1;
    my ($name,@seq) = split /\n/,$nextseq;
    my @aas = split //,join "",@seq;
    my @coords = getCoords ($name);
    print "$aas[$_] $coords[$_]\n" for(0..$#aas);
  }
}

sub getCoords
  {
    my ($fname) = @_;
    local $/="\n";
    my @ns;
    open my $fh, "<", $fname or die $!;
    while (my $line = <$fh>){
      chomp $line;
      my @ff = split /\s+/,$line;
      push @ns, (split /\s+/,$line)[0];
    }
    close $fh;
    return @ns;
  }
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