I think it would be easier for you to understand and debug what you are doing if, instead of symbolic references, you used eval, something like this:

my $assign;
$assign="(".join(",",@HeaderRecordNames).")=";
$assign.="unpack(\".join("",@RecordLengths[$RecordType])."\");";
print "Evaluating $assign\n"; # this is for debugging
eval $assign;
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While I assume (I didn't benchmark) that symbolic references would be somewhat quicker, I think this code is clearer and much easier to debug.