Graynomad:
That may have been the serial blocking, a non-blocking version might do a lot better although it will never match SPI.
I only read about this a few minutes ago in the context of the Teensy development board which provides up to 12Mbit/s full USB speed and non blocking serial.print calls.
So maybe a Teensy would be a good choice to read in the SPI data from the Arduino(s) and then send them to the computer.