I need for someone to help me creating a plan of attack ; )

Purpose: Setting up dual booting = Windows 8.1 + Ubuntu 13.10.

Present status:
Both OSs are installed in a different hard disks, with messed up booting files.

How did I get here (short version):
Days ago I had unplugged the Windows hard disk from the motherboard in order to reinstall Ubuntu, and keep things simple while doing it. It all went well, I ran Ubuntu successfully for about 5 days, after a good number of tweaks here and there I very happy with what I've got. My next step was to fix the Windows booting files.
Unfortunately I didn't think of unplugging the Ubuntu hard disk this time : ( As you may imagine, this messed up GRUB.
I was able to fix the MBR with the Win8 Repair startup USB key, using: ''bootrec /fixmbr'', but the following command failed: ''bootrec /fixboot'', it replied: ''The volume does not contain a recognized file system. Please make sure that all required file system drivers are loaded and that the volume is not corrupted''.
Additionally, I proceded to try: ''bcdedit /set {default} device partition=c'', but I got this: ''The boot configuration data store could not be opened. The system cannot find the file specified''
It was after this that my GRUB got messed up.

Where to now?
I have Boot Repair Disk, Super Boot Manager, and EasyBCD. Also a USBlive with Ubuntu 13.10.

At least for now, I don`t need actual details, but rather a clear layout of steps to take. Please consider what I want to accomplish, and where I am.
Example: Start by 1. Repairing the Windows booting files, successfully boot into Windows. Then 2. Do the same for Ubuntu: fix GRUB, then boot from a USBlive to run Super Boot Manager to setup the dual boot.
The above was just an example, and if anything a wild speculation of what's ahead.

Thanks a trillion guys!

JDL