Slow boot times, slow disk access, Laggy audio in games, constant crashes

Hey =D

I made an account to ask a question because i heard the community here is really nice.

Basically, I came back from singapore with a new built computer:
Asus PZ68-V Lk
Gtx560ti
Xigmatek 700w
i5-3470
2x 4gb Ram
The 500gb harddrive
Windows 7 home edition
(Some shitty case and fans)

So it was working fine and everything long story short it was all good no errors, no problems.

Then when i came back to my home computer (which is just a Hp pavillion g5470uk desktop with an i3-2100 but in a new case with another gtx560ti and 1tb harddrive) i wanted to merge them together to make a better computer.

So when i finished building it, it came to this:
Mobo: Asus PZ68-v lk
GPU: 2x GTX560ti
CPU: i5-3470
Ram: 8GB@ 1333mhz
HDD: 1x 500gb, 1x 1000gb

At first it didnt boot, so after some checking I found out that you cant boot off a harddrive that is new to the mobo without some pre-work. So when i booted it off the 500gb one (Which is the original one to the asus motherboard) the problem started.

I then took out the 1000gb harddrive to see if it would work, and it still was really slow. The only difference between now and then is when i launched arma 2-operation arrowhead it ran quite smooth. But now when i launch any game it runs smooth untill it has to pull new audio files .

Things ive tried:
Switching usb slots for all my devices
Updating windows
Updating Graphics card drivers
Defragging
Overclocking/Underclocking
I checked the bios and everything seems normal

Notes:
The boot time is around 10-20 minutes.
Everything crashes alot when you try to do operations especially steam and itunes.
When i am transferring files around its surprisingly normal speed but still quite volatile and freezes alot.


Sorry its mega long winded. Thanks! =D