I put the HDD LED Pin in the bottom right, the reset switch right next to it, and the power switch right above the reset switch. The writing on the pins face away from the board. This arrangement means there is a empty pin to the right of the reset switch and 2 empty pins to the left of the power switch. I hope that made sense.
My case doesn't seem to have a power LED.
Can anyone see where I am going wrong?
I've taken a few more photos of the motherboard if anyone could be so kind to take a look and spot out potential things I've done wrong.
I do believe I have your problem solved. It appears (from picture photo4ke) that you have a PCIe 6 pin connector into your ATX header on the motherboard. You want to use the ATX 4pin, 4+4pin or 8pin - may say ATX or CPU on it. The 6 pin, 6+2pin, or 8pin PCIe connector will not work there (+/- reversed).
You're quite welcome - thank you for the additional pics so we didn't have to guess all night.
As far as having the two HDD's with win 7 on them... On many motherboard it does matter which SATA headers are used for your boot drive (most often the 1st SATA bank is preferred). The computer will attempt to boot from the first HDD in the boot order. If that's the older HDD, the most likely result will be that the computer 'hangs' during windows loading (the OS is tied to the hardware), changing your boot order should fix that (if it happens). I think I would personally do a complete format on the older drive but you may have programs/data you want to access.