There are a set of protocols that disk drives follow and on top of that there are specific protocols used to encode drive commands and information over a USB link. Most drives follow a variation of the SCSI command set for drive commands, such as read, write, seek, etc. On top of this, the USB uses the mass storage class specification and typically the bulk transfer protocol, which specify how the disk drive commands get wrapped into packets of information suitable for transfer over the USB link. Consequently, the transfers are not performed in a PIO fashion.
In addition to all this, I am assuming you are using Windows here, the OS will enumerate the USB controller and determine its operating characteristics. It will see the device and vendor IDs and try to associate a driver with these. More than likely, it will think that the device is a disk drive and try to use it as such. You would need to write your own driver and somehow replace the standard driver with this. I firmly believe that windows was written with the idea that the people using it are complete and total idiots and that MS is second only to god. Good luck with getting it to accept your driver instead.
It would probably be significantly easier in the long run to investigate the many USB device controller chips and kits available today and use those as a USB to PIO bridge.