If you're splitting $_ several times before you get to matching the bit you want, the y/\n//c or matching $` for \n methods aren't going to work. I'd suggest prepending the line number (assuming you haven't changed $\ ;) ) when reading the file:

while (<FILE>) {
  s/^/[$.]/;
  $file .= $_;
}
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then do:

if(/(^\[(\d+)\](\S+)\s+(\d+)/m) {
  $mylist{$2} = $3;
  $linenumber = $1;
}
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Well, that's probably what I'd do (or something like it, anyway - I'd have to see the data to decide)