[ubuntu] Can't boot to installed partitions on MacPro 3,1

I've been unable to boot to my main hard drive successfully since upgrading from Ubuntu 14.04.4 to 16.04.1.

1. I apparently had a 'legacy bios' set up before the upgrade.
2. I have a number of different installations of linux on the machine
3. I don't have OSX or Window installed.
4. Post-upgrade I have installed rEFInd in hopes of fixing the problem.
5. I ran boot-repair via a live CD. The output can be found at http://paste2.org/6Uc778Gx
6. When the computer is started, I get a grub2 menu which, depending which option I choose, takes me to a rEFInd screen.
7. I have numerous options in rEFInd, but the only ones that work are for the 16.04.1 Live CD

I'd appreciate some help solving this problem and getting my computer back up and running.