The problem is most likely due to the Windows installation on the old disk is configured for the old motherboard, including the disk controller on the old board. You really should do full install, or at least a Windows repair.
BUT - Understand that if you "upgraded" your motherboard - that is, you did not replace the motherboard with the original maker's recommended replacement, and if your original Windows license is an OEM license, then that copy of Windows is tied to your old motherboard, and you MUST buy a new Windows license! Note that a new motherboard is considered a new computer, since the motherboard is the heart of the computer - UNLESS the exact same, or the maker's recommended replacement motherboard (if original has been discontinued or superseded) is replaced as part of a "repair" action.
Don't shoot me - I'm just the messenger! But that's the law. OEM, by definition, is tied to the "original hardware" and cannot be transfered to "upgrades".
Now if you have a retail copy of Windows - most people do not - then you can transfer that to your new motherboard.
I should have said in my original post that this computer is a custom built computer. So I don't think the OEM thing will apply.
The thing that's strange to me is that it doesn't recognize the drive at all. When I boot my computer from USb (I have a windows 7 zip drive that I configured) it brings up the windows installation screen just fine and asks where i want to install it to, but it doesn't bring up the old hard drive. is this because it's tied to my old mobo? or should it at least recognise it?