Hello Again Mr. Fallen Kell.
Don't file down anything. This is a very simple mod. Look at the plastic backplate from the Zalman mounting kit, and you will notice that in each of the four corners, the molding of that plate has a clearly defined rounded area. Within those rounded corners is a pre-installed metal nut which corresponds to the screw that comes through the board from the topside. The corner mounting screws pass through a hole in each of the four corners of the Zalman top mounting bracket, then through the board, and then into the receiving nut embedded in the Zalman bottom mounting plate.
Obviously, if you attempt to place the full Zalman bottom mounting plate on top of the existing Gigabyte Crazy-Cool 2 heatsink plate, the whole thing would be much too thick to be able to clear the motherboard mounting studs in most computer cases. And, all that rigidity is unnecessary, since whatever extra rigidity that might be needed to support the board from twisting/warping, is already supplied by the Crazy-Cool heatsink plate, which is itself adhered to and screwed to the bottom of the board.
So, what you want to accomplish is to use the benefit of the four rounded corners, with the embedded nuts, to secure the CPU cooler (whatever one you're using) to the board. The rounded corners even have a slightly raised area around each hole where the screw passes through to reach the embedded nut, that locks the whole works nice and tight into the mounting hole in the motherboard.
Therefore, just take a sharp hobby knife (Xacto knife, etc) and carefully cut those four rounded corner areas, with the embedded nuts, off the Zalman bottom mounting plate, and then further shave one of the cut-off corners down a bit more to fit in the pre-drilled hole on the Crazy-Cool heatsink plate, and then just mount the heatsink as you normally would do. It's really quite simple, and once you take a minute to look at the actual parts from the Zalman mounting kit, you'll immediately know what I am attempting to describe in this note. I don't know if you can use the Zalman upper mounting bracket as well, since I've never actually seen the cooler you intend on using. However, you may find that the upper bracket works, or can be modified to work.
Th first time I saw one of these Zalman mounting kits I was a bit skeptical, but after I used it once, I was convinced that it was a superbly engineered and designed item. Good luck and enjoy the mounting kit - it works! TheBeagle