I think that I found the solution to this problem. It was odd. I was troubleshooting last weekend and I noted that both drives were jumpered to be in “cable select” mode. This mode should let them automatically configure themselves as master and slave in the IDE chain and is the standard setting for my server vendor.
I changed the jumpers myself and manually set the master and the slave. As soon as I did that, all the problems went away. The initially RAID sync completed successfully and since then all installation activities have gone smoothly.
Very bizarre that CS mode caused so many problems for me. Regardless, I am happily up and will likely be returning the server to its co-located home in the next few weeks.