First, ++ to haukex for the post as it is most informative and detailed.

Now, which Arduino board are you using? Most (if not all) Arduino boards have their serial port connected directly through the USB connector. In fact, it's the same serial port one uploads new "sketches" to the Arduino with :)

You can literally plug your Arduino via USB cable (micro USB) to any USB port on a computer (Windows or *nix), and communicate with the Arduino over it using UART (Serial). USB is, after all, the Universal Serial Bus.

If you have further questions regarding the serial comms on the Arduino specifically, I'd be glad to try to help out. Just reply. Sounds like haukex has some understanding of serial comms in general, particularly using Perl, so that's great too.