I'm having a few relatively minor issues with my USB 2.0 ports. They function at the Clover menu, but turn off during boot. Once the OS X login screen appears there's about a ~10 second delay before they start working properly. All my USB 3.0 ports work immediately at the login screen.
My other issue, and I'm not sure this is related but if I have my GMYLE usb bluetooth adapter plugged into a USB 2.0 port, I get a full USB hub reset every 10 - 15 minutes or so. When it's in a USB 3.0 port there are no hub resets.
Otherwise all the USB ports seem to function correctly using PJALM's DSDT patches only.