Check the bios for hardrive recognition. Check both power supply leads to the hardrive and the motherboard to be sure they are seated fully. Older sata cables can come loose easily. IF the bios recognizes the drive, I use maxblast 5 to prep new drives; then you can do a fresh install or clone it. Be sure your boot order is set to cd>hardrive. Flash drives can sometimes mess up the boot order, and some folks have had issues with installing windows off a flash drive. Install only one drive at a time; older ide drives must have the jumper set to "master", and I wouldn't mix ide with sata until one of them has windows installed. After installing windows, with one ide and one sata, set the ide jumper to "slave" and make the sata the boot up device.