Check out Tie::File by our very own Dominus. His writeup sounds like exactly what you're looking for. I believe your code would reduce to:

tie @lines, 'Tie::File', $file or die "Couldn't open $file: $!";
for (@lines) {
  # actually modify the contents of the file
  s/66/$goodrow->{ClientID}/g;    
  s/0906\s406\s2427/$SIMCard/g;  
}
untie @lines;
[download]

-Blake