I assume the reason for it being USB is the lack of serial ports on the RPI!?
This is absolutely the problem.
I cannot find a GPS that uses SPI or I2C that has support for the RPi today.
One thought at the moment is to have an ARF with a SPI interface, thus freeing the UART.
There is already an SRF with a SPI interface, and the ARF is basically SRF + Amplifier