I found the schematic of Arduino Uno R3
see: http://arduino.cc/en/uploads/Main/Arduino_Uno_Rev3-schematic.pdf
The USB AVR you want to flash has already a crystal connected to it.
If the lines (SS, MOSI, MISO, SCK) of the Aruino Uno configured as ISP Programmer are connected to the ICSP header pins (Reset, MOSI, MISO, SCK) corresponding to the USB AVR on the second Arduino Uno, you should be able to program the USB AVR with avrdude.
Likely you have wrong ISP connections between the Arduino Uno as Programmer and the ICSP header of the USB AVR on the second Arduino Uno board.
The SS signal of Arduino Uno Programmer is available just on pin 10 not on the ICSP. You have to take this into account when you make the wiring.
Also, do not try to write anything in the 16u2 as long as this command:
c:\>avrdude -P COM3 -b 19200 -c avrisp -p m16u2 -n
returns error messages.