If your keys only go up to 43 how about this psuedo code

# open infile;
# open outfile;
for my $k_out (1..43) {
    for my k_in (1..43) {
        read $line from infile until /^$k_out $k_in/;
        write $line to outfile
    }
    set pointer of infile back to 0;
}
[download]

Clunky and slow, but it will not use much mem, or write temp files. A little caching sould help a bunch. Line starting ofsets would be a quick win

Cheers,
R.