Ghost array0 over to newly setup array1 problems

I should assume the CD drive is SCSI? What sequence is it set to come up in? Set it at 2 if possible. Have you checked, or better yet replaced the CD drive? Will it boot with ANYTHING else?
That Hiren's CD is not uuummm, kosher? People having problems booting with it and all, plus the utilities may not have full function anyway. No matter what, you will need to f/disk the destination drive. You will still need the CD drive to install the program too.
Backup software will still make an exact copy of your drive also. You might want to consider a little better product, especially concerning disaster recovery. not to get off topic but, a quote from J. Bolton on backup & recovery
"What will you do if a user overwrites a 1000page doc with a blank file with the same name? What will you do if one of multiple server apps goes bonkers? If the mainboard dies how will imaging get your system back? Do you stock a spare board so the image restore will work on the exact same hardware? After a system crash, Acronis True Image Enterprise Server allows you to perform a full system restore, a bare-metal restore or just a restore of individual files and folders.
Complete system restoration can be performed to an existing system, to a new system with different hardware or to a virtual machine. You could setup a whole new system and dump the image on that.