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I followed the instructions but instead of the solid blue light I get a flashing blue light. Any suggestions? I reformatted and did it over again but got the same result.

I had the same problem. Only blue blinking light. I solved it by doing this;
-Format card
-Extract the ML files on the card
-Download EOScard and set the bootflag there
-Delete bootable.fir file from card
-Run the firmware update from the camera.

Obviously if you want to uninstall you need to copy back the bootflag.fir file.

Question- During bracketing, can I keep the mirror up? so that it doesnt close and open between frames?

Great job. It makes the old 5d a whole different camera. Outstanding.