Not that you shouldn't try to find a faster or cleaner way to do this, but I'm of the opinion that correctness trumps speed. After you have a correct algorithm you usually can obtain faster speeds by parallelizing the task, and that's probably the best use of your time.

That said, here are some small improvements to your code that could result in better performance:

1) Use elsif where possible, i.e.:

if (/wire capacitance/) {
  ...
} elsif (/wire resistance/) {
  ...
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From your example file, it doesn't seem like you'll see both wire capacitance and wire resistance on the same line. Also, consider using elsif in the other chain of if statements if only one condition can be true at a time.

2) Use: if ($TotalNets % 50_000 == 0 && $TotalNets > 0) ... to test if you want to print out the trace message. It's simpler, cleaner and faster.