To address your question #1 first: You forgot to reset $i to 0 before moving on to the next record. Add:

    $i = 0;
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at the end of the loop where you are reading from the array and printing the values out.

Having said that, I'd use array of hashes instead of array of arrays to store such data. Hashes lend themselves very nicely for storing records.

#!/usr/bin/perl-Tw

use strict;

my @dataA  = ("A1", "C1", "S1");
my @dataB  = ("007", "008", "005");
my @dataC  = ("999-99-9999", "888-88-8888", "777-77-7777");
my @dataD  = ("self", "spouse", "son");

my $count = 3;
my @major_PER_Data;

# save it
for (0 .. $count - 1) {
    push @major_PER_Data, {
               ID => $dataA[$_],
               CUST => $dataB[$_],
               SSN => $dataC[$_],
               RELATION => $dataD[$_],
              };
}

# print it

for my $PER_item (@major_PER_Data) {
    print "$PER_item->{ID}\n";
    print "$PER_item->{CUST}\n";
    print "$PER_item->{SSN}\n";
    print "$PER_item->{RELATION}\n";
}
[download]

Much smaller and clearer.

/prakash