|Save any data you may need on one of the drives, the one you aren't going to use for installing windows on, if necessary.|
Stick 1 and only one hard drive in the new computer (keep it simple)that you want to hold the windows operating system, then go into the bios, under "Boot" (usually) and make sure cd/dvd option is enabled and listed before the hard drive. Boot to the dvd and install Windows fresh. As mentioned above, you cannot install windows on one system for example that has an AMD board, c-media audio, Nvidia on board graphics, etc, take it out and put it into a machine with an intel board, intel on board graphics and realtek audio, it will do just what is happening to you. You can sometimes repair it and make it work, but how you are doing it is wrong. When you get Windows installed, and rolling good on the new system, reboot a couple of times make sure it boots fine, then shut it down. Now you add the second hard drive. Boot up, if it boots up to windows fine, it will install the drivers for the 2nd hard drive and you are good to go. If you get an error on boot up after adding the second hard drive suddenly, the bios may be attempting to boot from the "2nd added hard drive" instead of the 1st one with the fresh windows install. You would have to change that in the bios, no biggee, but as you have been doing it produces the results you see. Best just to start with the one hard and then the system is not confused as to which hard drive and neither are you.
To err is human but to really screw things up, you need a computer!
message edited by HopperRox