Haf X Computer Case Problem

I'm building a computer. I ordered a the new Cooler Master Haf X Computer Case. It comes four fans, with room for an optional fifth fan on top. I bought the extra fan as well. It is exactly the size that is supposed to go in the extra fan slot. it is also from Cooler Master. After inserting the fan on top and screwing it into place, I was ready to put the top of the case back on. There was just one problem. When trying to put the top of the case on, the cables coming from all the ports were keeping the top of the case from snapping shut. I found that the fan covered up a small portion of the slot where the cables run from the ports on the top of the computer to the inside of the computer. As well as that, there were more notches on the fan (that were there for using this fan on other cases) that the cables were hitting. I looked to see that some of the fattest cables were two USB 3.0 cables. Taking them out, I was able to snap the case back on. I would really like to have these cables plugged in. I got a motherboard with USB 3.0, and even if I didn't have a USB 3.0 device, they still are perfectly good as USB 2.0 ports. However, I do not want to take out the extra fan, which I know is the correct size and model for that fan slot. I would also like to avoid buying new cables or modifying my case. It doesn't appear that anybody else is having this problem as far as I can see.

If you have this case and added the extra fan, could you please tell me how you ran the cables so they didn't have the problem I described. If you had the problem, please explain how you fixed it, even if it involved buying new cables/modifying your case/fan.