It's easier that that. When you get your new machine built, make sure you install ONLY the new HDD in it at first. Install Win 8.1 on it and get it all working. After that's done, shut down and add the old HDD. When you power on, go immediately into BIOS Setup to where you set the Boot Priority Sequence. Most people would set it to try the optical drive first, and then the HDD you want to boot from (the new one). Make sure the old HDD is NOT in the sequence. SAVE and EXIT from here, and your machine should always boot from the new drive, and never try to boot from the old one.
The reason to set the optical drive as the first device is this: under normal circumstances with no bootable disk in the optical drive, the BIOS will check that drive first, find no bootable disk, and jump quickly to the second device (your new HDD). BUT in odd circumstances (like, your HDD appears to have failed) you can place a bootable CD in the optical unit and boot from it.