Fortunately someone made a tool that will take the U3 tools off of the USB. This is necessary because I couldn't make the USB stick bootable with this software on it. In Ubuntu it was just an easy:
sudo apt-get u3-toolcommand away. The directions on how to use the tool can be found here: http://goo.gl/kqcjAs on the wilderssecurity forum. So with just a few keystrokes the USB stick was now clear and ready to be formatted and made bootable.
I looked at a few different options to make the USB stick bootable. I tried using Tuxboot first, but it did not work for me. After a little more looking around I found Multisystem via pendrivelinux.com They have a simple walkthrough on their website where the software can be downloaded too, it can be found here: http://goo.gl/zwNVSd
After that it was simply following directions and installing a few .iso files. I opted for putting Clonezilla, OSFClone, Gparted, and Trinity Rescue Kit on it. Just so I have options. (Gparted is not disk cloning software but allows the resizing of partitions on a hard drive) Another option would be to put on just a generic Linux distribution and use the "dd" command in a terminal. I may consider that in the future, but for my first attempt ever at cloning a HDD I would rather be walked through the process.
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