These wacky installation hijinks are why you run into issues booting in the first place.
I read through your previous post again (here), to which a solution was not marked but as you left the thread it sounded like you were going to set up a custom.cfg to get Grub to pick up the second drive. Did you do that? Because if so, you will have to take down the custom.cfg now that the boot entry it is pointing to is gone.