Segmenting the code would be no problem compared to the logic we had to pull toghether to work with the restraints of the RS-232 original version.

If you can tell me how to turn off interruptions so the USB I/O is only processed when we tell it to, I'm confident we can do it. I would need to know the time limit between polls too of course.

I presume you are using the microchip application library version of the firmware? If so then you can find detailed information over on microchip's forum. Really it's just a case of setting the interrupt configuration define to false and then polling the USB routines at least once every 200mS (if I remember correctly!). Again it should be covered by microchip's documentation.