On the GPU, I have it plugged into the first available slot on the top. Looking at the motherboard, there are two other PCIEX16 slots, but the 3rd one is at the very bottom so wouldn't work. The 2nd one down might work, but you would cover up a PCI2 and PCIEX16 slot, so not certain about that one.
I don't know what mobo you have, but most P67 or Z68 are going to be the same. The top slot will be a x16/x8 slot, as in, with a single card the slot will run with a x16 bus speed but in a dual card setup it will only run at x8 bus speed. The second slot is a x8 slot, if you wanted to use the second slot it would limit your card a little but not dramatically. The third slot is going to be a x4 slot, this is meant to be a PhysX slot or it can be used with pci-e x1 devices. You wouldn't want to use the third slot for a single card setup.
As for the Noctua NH-D14 and the Corsair Vengeance memory, I wish I had known exactly what you ordered first as I could have warned you. I took the heatspreaders off my Corsairs and then I trimmed the heatspreaders down with a dremel. I should bought the Ripjaws and I will next time but I had originally planned to use a different heatsink but it just didn't work as good as I was hoping.
I would of ordered this memory and it's priced right.
Newegg.com - G.SKILL Ripjaws X Series 8GB (2 x 4GB) 240-Pin DDR3 SDRAM DDR3 1600 (PC3 12800) Desktop Memory Model F3-12800CL8D-8GBXM
The Marvel 6Gb/s controller is alright but it's a little slower than the Intel 6Gb/s controller.
Throw that black bracket out of a moving car
You should take some time to properly route your cabling, not only does it look like crap but it blocks your airflow and traps heat.