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The Cat6 plugs are slightly different from Cat5 plugs. If you ran Cat6 cable, don't cheap out on the plugs. They're not that expensive. Get some shielded Cat6 plugs. Theoretically, it could impact the speed.

Not much experience in this department, but I was looking for a very similar answer. Here is a question over on stack exchange which might give the answer you're looking for: http://superuser.com/questions/663732/can-i-use-cat5e-jacks-with-cat6-cable

Thanks! From what I'v found they have the same 'pinout', just different 'quality' specifications such as twisting, shielding, ect.

Haha it's okay you'll learn quickly!
 
The pairs are the same - 4 pairs of cables inside a sleeve. In Cat6 you have a plastic core which separates these 4 pairs (in the shape of a +), tighter-twisted pairs, and a slightly thicker jacket to reduce cross-talk. In some Cat6 cabling the internal copper cable pairs are slightly larger.
 
I've gotten Cat6 into Cat5E RJ45 connectors fine before, personally never seen a speed difference so just use whichever I have in the bag!

Ahhh. Thanks for asking all this though, i'm planning on setting up my own network soon and this'll help me a lot with it! Thanks bruh.

It's the cable that will make the difference generally.
 
In my experience I've regularly used Cat5E cables and gotten Gigabit speeds through the network. I've also made custom cables with both Cat5E and Cat6 and speedtested using a file transfer and got pretty much the same results. I've also used Cat6 patch cables on 10GBASE-T and gotten near-on that over a distance of about 10m.
 
The thing that will make the biggest difference is the quality of the cabling. Buy good quality cables or components to make them, and you shouldn't see any limitation.

Thanks! From what I'v found they have the same 'pinout', just different 'quality' specifications such as twisting, shielding, ect.

Color matching, niceee.

The ends of a network link will attempt to work at the speed they are configured for (if configured/configurable), or autonegotiate to the highest common speed. If the electrical performance of the link between the parties is not good enough, you get errors. Very rarely do I see switches drop down to a lower speed, and when they do, it is usuallly 10Mbps.
 
The switches only see the electrical performance on the link, not what is printed on the components:
I have a bit of experience with running networks on old cabling. Work has ~40 switches, and the edge cabling and termination that goes with that, all cat5 from the 10Mbps era. Not cat5e, plain old cat5. The 1000BASE-T spec allows gigabit on cat5, and it does work, but with no margin for maximum length runs. cat5e has (from memory) stricter crosstalk specifications, with leads to some margin. 
 
As Xineas notes, as far as the 8P8C connector goes, the 'cat6' one accomodates thicker wires, which in turn allow higher PoE power limits. As far as actually crimping it onto a cable is concerned, I find that a tightly-twisted cat5e connector on cat5e cable will run 10Gbps, whereas a cat6 one with the twist of the cat6 cable unwound too far will give me errors. So take care and make pretty terminations, they matter.
If you find yourself in a situation where you are running 1Gbps on cat5 (not 5e), or 10Gbps on cat5e (which is not officially an option, as the cat5e requirements are not strict enough), I very strongly recommend some level of management on the switches. Without it finding that defective link becomes impossible.

I don't know all the answers, but I can answer 2 of them.
 
As far as SSDs go, it depends on the workload your doing: Reading tons of tiny files is not the strong suit of any SSD as far as I know. General use and just dinking around, they rock. 
 
If you are buying it just to "have" a server then save your money and use what it comes with for storage.
 
PCI-X was mostly used as a connection between servers or banks of servers. If you only have 1 or planning on having one for awhile it's not an issue. If you want to link up a bunch of them then yes, it's good to have.

If i don't build my own, I'm probably going to go with one of these. Thanks.

I'm not sure about space. It will keep your old install of 7 for a month in case you want to roll back. But I'd do a clean install anyway after the upgrade. In-place upgrades have caused problems.

The old installation should be put into a Windows.old folder. Everything from your previous installation would be found there and the folder is removable.

Ok, cool. Thank you for your help!

you don't need a raid controller if your motherboard is Asus Z87-A