There are quite a few problems with your code. The first you need to sort out is where you read in the data:

push @data, V(split) while <$in_fh>;
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You are creating one vector from all 6 points on each line, when you should be creating two vectors for each line:

while (<$in_fh>) {
    my @points = split;
    push(@data, V( @points[0,1,2] ), V( @points[3,4,5] ) );
}
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Now your @data can be looped through and you can perform the calculations on the vectors.