The extended boot time isn't the only issue, if I change the hard drive order at all, the system refuses to boot.
Your motherboard doesn't "see" the System Reserved partition; that's why it doesn't boot when you change drive order.
When do a fresh Windows install, Windows creates a System Reserved partition (normally around 100MB) that's used for system startup. If you have a HDD connected Windows will mistakenly create the partition on the HDD instead of the SSD.
You said there's no partition on either drive so I don't how that happened.
Sorry, don't know what else to suggest. Hopefully other Forum members will be able to help.