Soooo, after almost a week, it happened AGAIN.
I booted from my old disk, opened up the EVO 960 and looked inside the directory. the System folder was inaccessible! I couldn't even cd into from the terminal. After looking all over the place for a way to repair permissions in sierra. Finally I just chmod 755 the System folder and what do you know? It booted and appears to be fine. This is obviously not an issue with the drive, but have you ever heard of this????? It only started happening once I installed this new drive.