Using a floppy drive bay looks like a reasonable solution but won't work for me since my mini-itx case does not have a full size floppy bay (it does have a slim floppy bay, though).
After doing some research it appears to me modding the USB 2.0 port will require some major surgery. One solution might be to replace the USB 2.0 port with something like this
and solder the wires from a USB 3.0 cable to the pins. Another solution might be to gut the innards of the front panel USB 2.0 port and use the original metal housing to clamp down on female end of the USB 3.0 cable.
Thanks for the suggestions.