Oy! I have spent all day trying to solve this problem and it's only got worse!
Background: MacPro3,1 with a separate HDD for OS's.
No Mac OS, but multiple versions of Ubuntu (14.04.1 -fresh install, 14.04.1 upgrade from 12.04.5, and 12.04.5 for safety).
Problem #1) Mac will no longer boot from CD ROM.
Problem #2) Grub configuration is screwed up such that the UUIDs in the grub.cfg for 14.04.1 upgrade and 12.04.5 are really for the 14.04.1 fresh installation. I've run grub-mkconfig multiple times to no avail.
Additional information: I've got boot-repair installed, but don't know how to configure it correctly (and not even sure if I should use it). The output from it can be found at http://paste.ubuntu.com/8049643/
If someone could help me solve these problems, I'd appreciate it.