Yup, your problem starts right at the first line as you suspect. What you have is not Perl even though you state you "want to explore a smart perl approach". Here is a sample Perl program that demonstrates the techniques you need to implement your task:

use warnings;
use strict;
use Data::Dump::Streamer;

my $str = <<SNIPS;
Hello all, I am encountering some issue in trying to do the following 
+in ksh88,
therefore I want to explore a smart perl approach, but my knowledge is
+ limited,
can you help?
I have 2 files, the first (indexFile1) contains lines with start
offset and length for each record inside the second file, so just 2 nu
+mbers
separated by a space. ...
SNIPS

open my $recData, '<', \$str;

while (<DATA>) {
    chomp;

    my ($start, $len) = split;
    my $segment;

    seek $recData, $start, 0;
    read $recData, $segment, $len;
    print "$segment\n";
}

__DATA__
16 12
80 9
315 10
[download]

Prints:

encountering
therefore
separated
[download]

Note, to avoid needing external files I've used a string to provide one input "file" and provided the other as data following the body of the script. Note too that I tested this under Windows so you may get different output if your OS uses different line end characters than Windows does.