Actually, 5.9 for disk is an outstanding rating! The only way you can really increase that is to use a SSD for your boot/OS drive instead of a standard hard disk.
Your other scores are great too. I think the problem is not your scores, it is how the WEI tallies and presents the "Base Score". It makes it appear as though your hard disk is creating a monster bottleneck and dragging your whole system down, when in fact, it is not.
Bottom line - you have great scores. Don't worry about it.
Another reason to not worry about them is they are bound to go down - well, they will stay the same while new computers will achieve higher scores. Why? Because as the state-of-the-art improves, and faster CPUs, graphics cards, and mass storage become common place, Microsoft WILL slide the maximums achievable up again.