Welcome to the community, SaltWaterGator!
I'd recommend you to try unplugging your old HDD and making sure you will boot flawlessly without it. Since you've used the software to clone to the system, you should have a System Reserved partition on the new drive as well.
If you are able to boot without your old drive being plugged via SATA to the motherboard and it just has this System Reserved partition on it left after the migration/cloning, you could re-format the drive so that you'd use it as secondary storage.
Here's a tutorial that explains how to partition and format the drive for that purpose through Disk Management:
http://products.wdc.com/support/kb.ashx?id=Op9p2S
Hope it helps. Keep me posted!
SuperSoph_WD