Yeah, you're just using the "Run the RUU" step of those instructs only. It does reference being in fastboot USB in hboot but that's just an alternate way of doing it and comes in handy if you're phone is soft bricked at the time. Since your phone is alive and well, you can go the old tried and true route of just running the RUU while the phone is normally booted in charge only mode.
Yeah recognition is always the PIA about this. Since you got HTC sync, it comes packaged with the drivers for usb recognition. Look on the pc at add/remove programs and see if there is a separate little driver package. If so, remove the main HTC sync program. You don't need it and it could potentially interfere with the RUU. Then, with the phone still hooked up to the PC (charge only and usb debugging enabled), reboot the pc. When the pc reboots, it should recognized the plugged in device and apply the drivers automatically.
If that doesn't work, we can try to force the driver update in device manager next.