rayp

Wack

Boot sector is on the C drive, so that's perfect. 
I'm afraid there's little we can do to speed it up.  It's probably just the BIOS/UEFI that's taking time to check the hardware ... which includes spinning up the HDD to check its health. 
 
If it makes you feel any better, your PC still boots in less than half the time that mine takes, and mine only has SSDs inside with a 960PRO as boot drive.

The HDD size issue is caused by the difference between the MBR and GPT partitioning styles.  Now that yours is using GPT, you shouldn't have that problem anymore unless you manually change it to MBR in diskpart.
 
As for why it's best to install Windows with all drives unplugged : If you install Windows on a PC with more than one drive, the Windows installer has this nasty habit of installing the bootloader on another disk than the one you're installing the OS on.  If the bootloader is indeed on the HDD, that could very well explain slow boot times.
 
That being said, normally the BIOS/UEFI always checks all the detected hardware before it starts loading the operating system.  So that might also explain why you hear the HDD spin up before the OS starts to boot. 

I'm guessing most of your slow boot time is waiting for the BIOS splash screen to appear? Once you see the Windows Logo it's pretty quick to load in to the desktop?
The motherboard most likely is checking connected SATA devices during the POST process. In layman terms it's poking the HDD asking if it's alive and waiting for a response; which may take a few seconds as the drive needs to spin up first. Doesn't matter if the drives are the boot drives or not, any connected storage drives will be checked.

AFAIK there's not much you can do about it. You can't tell the motherboard to ignore things during POST. The above suggestions of reinstalling windows won't help since it's a delay before the system even tries loading the OS (unless you have accidentally installed windows on to the wrong drive).