Writing your new file line by line is just fine. I'd arrange to set $\, the output record seperator, to "\n" just to avoid having to print it explicitly. You place the seperator at the front of each print, which I would avoid. You'll probably also want to set $, for the output fields.

You can get buffered input of your fixed length chunks by setting local $/ = \1034;. That will avoid the fussiness of working with read.

It'll look like this:

{
    local ($\ , $, , $/, $_) = ("\n", "\t", \1034);
    my $somefmt = 'ccc v V '; # add the rest of the format
    open my $in, '<', '/path/to/original.dat' or die $!;
    binmode $in;
    open my $out, '>', '/path/to/outfile.txt' or die $!;
    while (<$in>) {
        my @data = unpack $somefmt, $_;
        # ... adjust @data
        print $out @data;
    }
    close $out or die $!;
    close $in or die $!;
}
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