RAM:The motherboard recommended is not X99, right?
The MSI motherboard I recommended is a z170a board, which is a newer chipset that the X99. Basically, that "Optimized for X99" is marketing, the ram I recommended is the likely the cheapest you will be able to find at 16 gig. You can get
8 gig cheaper, though in this case, 16 is a better value. I recommend Kingston because they have the most robust testing on all their memory before it leaves the factory.
POWER:Would that be the case with my HAF932?
You want those longer cables with that big case! I have never built a rig in a HAF932, so I am not sure just how long you will need, but you can buy some extension cables if you need them for some connections.
MOTHERBOARD:What are I/O ports?
Yup, just what
@Merciless Mark said, basically anything you plug in to the motherboard externally, like your mouse and keyboard. The I/O sheild is a little piece of metal, with the correct size opening cut out, that covers the ports to keep out dust.
CPU: Do I really need this and will my computer think I have two GPU's?
You will indeed have two GPU's and you should be able to switch which one you are using by a setting in the BIOS, though I am not that familiar with MSI. The built in Intel graphics is fairly decent, and is a good backup if your video card fails.
Newegg/nl/ has a rather limited selection on motherboards, this
Asrock Z170a would be a good alternative.