I think the problem has to do with the fact that I am using the $type variable which is declared in the if block, and the $B1 and $B2 variables which were declared outside of the if block.

Half-right. The problem is that $type is declared in the if block, but it's used outside of the block.

     my $type;
     if ($B1=~ /^\*/ || $B2=~ /^\*/) {
       $type = "S";
     } else {
       $type = "I";
     }
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or

     my $type = $B1 =~ /^\*/ || $B2 =~ /^\*/ ? "S" : "I";
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or

     my $type = grep(/^\*/, $B1, $B2) ? "S" : "I";
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• You're confusing eq (string comparison) for = (assignment). See perlop
• | is for bit math. You want ||. See perlop
• "*" is a special character in regexp patterns. You want "\*" to match that character. See perlre

I didn't read any further. Hopefully, that will give you a good start.