Oh, duh. The filter beads are on the power and ground, not the data lines. So, that answers that question. I actually misrepresented this design, in that it was my girlfriend's design, not mine. So that's why I didn't realize what the filter beads were connected to.
So, this seems to be the correct way to implement the USB hardware: data lines straight from USB connector to PIC microcontroller, with no passive components at all in between because it is already in the USB module in the PIC. Filter beads on power and ground, Possibly a capacitor on the connector shell to ground, or possibly a resistor or a solid connection, based on whatever reduces EMI the most. And some ESD protection diodes on the data lines. That's what I'm going to do.