my $PERcode =  (split(/,/,$line2))[0];
    my $FDXcode =  (split(/,/,$line2))[1];
       ...
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is better written as

    my ($PERcode,$FDXcode,...)= split /,/,$line2;
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Apart from that I really have a hard time understanding what you want to do, especially since you put everything in code tags. For example, what is this:

if 
field1 ne "" 
field7 ne ""
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Is this the code your are trying to parse? Because it doesn't look like perl

Would it work for you if you wrote just this:

if ($CODE1 eq $PERcode) && ($QSIGN1 eq '' or $QSIGN eq $QSIGN1) && ($A
+SIGN eq '' or $AMTSIG eq $ASIGN) ...
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This ignores any empty fields and just compares the fields that are set

UPDATED