After reading more about this, I decided to start over and try a few things:
1. I made sure and stopped my array before shutting down
2. I downloaded and used the "Open Files" app to see what else I had opened
3. I stopped all Dockers
4. I followed the guide here to update the timers
Then I did a shutdown, and it worked perfectly!
I was unaware of just how easy it is to have an "Unclean shutdown", that then effects your booting back up!