Here's a suggestion to avoid a problem later. When you are building the machine and go to Install Windows on it, do NOT install the old HDD. Install ONLY the new HDD in the machine. This applies to Win 7 and 8, not earlier.
Why?
When Install of Win 7 or 8 is done, it does this by default: it looks for a second HDD. If it finds one, it install there a semi-hidden copy of key OS files before putting Windows on your main drive. The idea is that, sometime in the future if your main drive's OS files become corrupted and it can't boot, it will go to the backup copies on the other drive and use them to restore the main drive, then complete the boot process. It automatically fixes that problem for you! Nice Idea!
BUT (there's no free lunch!) the problem some have had is this: EVERY time the machine boots it checks to be sure those backups are there, and, if not, it will not boot! So if you remove the second HDD for any reason (like, maybe your old HDD failed), your machine suddenly does not work. (There is a cure for this, but I'm giving you a prevention.)
HOWEVER, if you do the original Install with ONLY the one HDD in the machine, it can't put the backups on a non-existent second HDD. It puts them on the only HDD present, which is the one you will always boot from. AFTER you have Windows installed and running, you install your other HDD(s) and they work. If you ever remove the extra HDD(s), no problem. The downside of defeating this part of the safety net is that the backups are on the SAME HDD as the OS, which is a bit less secure than having them on a separate HDD in the system.