Now that we have the pushpins removed, will will want to put the size 6 washers onto your M3 bolt, either purchased at your local hardware store, or using the ones the came with your mounting kit. Then, put them through the mounting bracket in the same fashion that the pushpins were, and place your cooler onto your motherboard as if you were mounting it. Then, thread the screws all the way through the bracket (they will be far too long) until the cooler is at the tightness you would like. Tighten them down alternatively so that you will have even pressure. So turn screw one a certain amount, then do screw 2, 3, and 4 in the same fashion to ensure even pressure.
Once you have all four screws tightened an even amount, and to the overall pressure desired to mount your cooler (careful not to tighten too much where your motherboard starts to flex), it will look something like this:
Next, you will want to mark off the lengths you will want to cut down to. I did this by taking a fine point sharpie and coloring the threads as close to the bracket as I could.