[dnanian]

They should both be on Cable Select -- that way, they set their master automatically.

OK: what I'd do is Smart Update the backup. Then, rename it to the same as the startup drive and set it as the startup, but don't restart.

Power Off. Then, hold down Cmd-Option-v and power on. Keep them down, and it should go into "Verbose" boot, which will hopefully tell us more about what's having trouble.