The only thing that is not brand new is the hard drive. The only connections I have to the motherboard is the hard drive, cpu fan, front panel header (pw, speaker,hd, res), 2x12 main power connector and 2x2 power connectors.
Because your running the same Cpu and mobo. One other thing i might suggest is if you have a spare system(assuming that you still have your previous Rig) to test you HDD on, i'd do that before buying another.
Your new system has the same Motherboard & CPU as your old system? If not, then what is probably happening is the old HDD still has the drivers for the old motherboard & that is conflicting with the new one. The only way out of this is to do a clean install of windows.