Best practice is to do a clean installation of Windows from scratch.
First test hardware outside case. If everything is OK put them in case. Do necessary setup and configurations in BIOS.
Then do a clean installation of Windows on the drive you want to be system drive. If you have an SSD and install Windows on that, unplug and disconnect any possible number of HDDs you might have before installation. (Power off and unplug PSU from wall outlet before disconnecting and re-connecting HDDs from and to the system.
Connect them back after you install Windows and motherboard, chipset, audio and GPU drivers.