The only way around it would be to perhaps get combination cards such as USB2.0 & firewire, or remove say the sound card and get an external USB sound card. Other than that I think you will need to upgrade the MoBo to one with less onboard features and more PCI slots.
I'm not expecting a lot. A 'normal' file (700Mb) transfer via FTP from one machine to the another would take about 3 minutes from 100Mbit/s to 100Mbit/s network interface cards (that's roughly 28Mbit/s). That is also just 25% utilisation.
With the USB2 (note: not 1) to 100Mbit/s ethernet, this takes about 30 minutes. That's ten times slower! What is going on?