Alan, are you sure you need to change those BIOS options for PCIE to operate normally? Do you have a PCIE graphics card in a PCIE slot?
Try running GPU-Z. It will report the PCIE bus type and usage.
As for the original topic: You can use a USB3 external drive with USB2 ports. My mainboard doesn't have USB3 either. You will lose some speed though.
Also, I am pretty sure there must be USB3 expansion card that will fit in regular PCI slots. No need for tinkering with PCIE (I hope).
And another thing comes to mind. If you are tinkering with those obscure BIOS settings, the BIOS optimization guide could come in handy.
Regards.
EDIT: I forgot to mention that any BIOS out there is different. My Gigabyte BIOS doesn't have those options you mentioned.