Chosen Solution
I added a Samsung 500 GB EVO SSD using the ifixit.com kit. I put the new drive in the new slot, but with the old cable, and put the original HDD back in its place but with the new cable. I performed a new install of El Capitan on the new drive. I now seem to be encountering occasional kernel panics coming out of sleep mode. Has anyone else experienced this?
Configure the new equipment in the exact same place that the older parts were. If that doesn’t work then you may have to use the older hard drive as your primary boot device.