Got a new hard drive, cloned my old one to it but can't boot.

[Unkle Dada]

I recently got a 2TB HDD to replace my almost filled up 500GB HDD. I don't want to have to dick around with multiple drives and partitions, so I decided I was gonna clone my original HDD and replace it.
Anyway, I cloned it with ShadowCopy and changed the boot drive to the new one in the BIOS, but then I got the inaccessible boot device error.
Oh well, I popped the Windows 7 install disk in, but it doesn't let me install Windows without deleting the contents of the new drive, after waiting hours to clone it. I pressed the upgrade option and it told me to reboot and let Windows run normally, which I can only do from the old drive.
Is there any way to make the new drive bootable without having to re-clone?

[editline]30th December 2014[/editline]

After a googling session I've figured a couple of things out.
1. I didn't clone the system reserved partition, only the C:
I copied them over afterwards on an unallocated partition on the new drive, but it still wouldn't boot properly.
2. I formatted the new HDD before I made the clone. It wasn't showing up in explorer so I thought I was supposed to do that.
3. I haven't even changed the SATA cables around to make the new drive the primary one.

So, unless anyone have any input, I will likely have to go for removing the partitions and try cloning again properly tomorrow.
BTW can anyone recommend any good free cloning software?

[Spankys]

Download Hirens Boot CD and make a bootable CD or flashdrive. It should have several cloning tools in the backup category.

That thing has saved my ass so many times, its a great tool to have laying around for the future too.

[Unkle Dada]

Unformatted and re-cloned with the system reserved partition too. Booted up with no problems.
Never format before cloning I guess.