Gonna respond in quotes if I can get it right so I can answer questions easier.
Windows should be installed on the machine it is expected to run on. It sound slike this is not the case here. There are just too many variables involved for it to cope.
The hard drives in both systems are the same so Windows is definitely installed. I actually had to take the new parts out and put all the old stuff back in so I could access the internet to see if I could find some help. I am not 100% sure but I think the issue is that while they are in a RAID now on the old system when I attempt to boot with the new system it isn't recognizing the RAID so it thinks it is a fresh install.
You might try a repair install. Do you have a real Windows CD?
Yes, but it is a Windows Upgrade CD. Would that work?
Other possibilities are an incorrect build or other hardware problems. There are too many variables here all at once. It needs to be simplified. So recheck EVERYTHING and then try to boot with just the CPU/fan, video card (if not separate) and one stick of RAM. Does that boot? Windows will not fix a hardware issue.
Not 100% sure, do you mean try and boot without the hard drives and see if it will go to BIOS? Or just remove all the un-essential parts and see if it will boot to windows?
I appreciate the quick response.