To flash the bootloader is just way too easy.
Step 1 install Arduino (the IDE Integrated Development Environment)http://arduino.cc/en/Main/Software
Step 2 install the driver for the USBtiny
For windows, we use a modified LibUSB driver. You can download it here:
http://www.ladyada.net/make/usbtinyisp/download.html
•Windows USBtinyISP driver built with libusb v1.12. The windows binaries below are built for this driver. If you want to use the latest WinAVR use this!
•If you are using 64 bit windows Vista or 7 (or you're just plain having annoying problems with the driver above), try the Windows 7 x64 bit driver. You'll still need to click the button taht says "install anyways" when it complains its not verified.
Step3, Connect the USBTinyISP
Unplug all wires going to the EC board. Ensure the jumper on the USB tiny is set to POWER the board (jumper over the 2 pins on the USBtiny)
Plug in the USBTinyISP and connect the 6-pin ISP header to the board. Do not use the 10-pin header. The 10-pin connector on the extruder is for the quadrature encoder, not burning firmware!
You should no see at least the 5 volt LED light up on the EC (Extruder Controller) board.
Step4 Start the Arduino software. From the Tools>Board menu, select "Arduino Deicimila, Duelminove, or Nano w/ Atmega 168". Then, from the Tools>Burn Bootloader menu, select your ISP programmer (USBtiny). The Arduino software will begin to upload the firmware. Ordinarily, this will take two to three minutes to complete, so be patient.
Again from Adafruits site for the USBtiny
There are two LEDs, a green one near the USB port and a red one near the cables.
The green LED indicates that the USB connection was sucessful. If the green LED doesn't ever light and you're sure its in right, there was a problem with enumeration. If you're using a Windows or Linux machine and the green LED does not light up when you plug it in, theres a problem. If you have a newer Mac OS machine, try sending it commands via avrdude - the LED should light up then (strange but true!)
The red LED indicates that the USBtinyISP is 'busy' programming. You probably don't want to unplug it or the device being programmed while it's lit. However, if there's a software crash the LED may remain on even though its not doing anything.
When you're done, you'll see the "debug" LED on the board flash periodically.
NOW you should be able to use replicator-G to upload the firmware normally after you unplug the USBtiny and plug in your FTDI cable