grub2 - GRUB not booting correctly after dual boot install

I followed these instructions to dual boot windows 8 and ubuntu:

Installing Ubuntu Alongside a Pre-Installed Windows with UEFI

I was successfully able to install ubuntu. But then I couldn't boot into windows 8

  "File: \Boot\BCD Status: 0xc000000c Info: the boot configuration data for your pc is missing or contains errors."

So I ran boot-repair in ubuntu.

But then when I restarted computer I get:

error: invalid arch independent ELF magic
grub rescue >

At the end of boot-repair I had this message:

Please do not forget to make your BIOS boot on sda2/EFI/ubuntu/shimx64.efi file! 

I have no idea how to do that. I am able to boot into ubuntu by hitting the F12 on startup, otherwise it goes to the screen with the invalid arch error.

Here is the summary of the boot-repair: http://paste.ubuntu.com/6535680

EDIT: Still not able to boot into windows 8 from grub screen btw I get:

error: unknown command 'drivemap'.
error: invalid  EFI file path. 

EDIT: A few more details: when I installed ubuntu I had my BIOS set to legacy mode (not UEFI) as suggested by the article above. When I installed Ubuntu I chose the "Install Ubuntu alongside Windows 8" option.