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I hate to answer my own question, but noone else has and I've worked on trying to solve my issues.
The only way I found to get QT Creator to work was by not using a CMake project type. Instead, I went to: File->New File or Project->Import Project->Import Existing Projects and selected to choose all files/folders included in the project.
QT Creator creates a few files in your project, one being a PROJECTNAME.includes file. I added the paths to my necessary include directories (e.g. /opt/ros/fuerte/includes), as well as my third party include files, and the gen_msg proper folder for my custom messages.
This solves all of my issues above, except (and I dont know why yet) the boost code completion. It is a little annoying because you have to modify your CMakeLists file for building and then your .includes file for code completion (unlike a CMake project where you just modify your CMakeLists file only), but it was exactly the same amount of work as my other option: eclipse (which I'm not necessarily a fan of).
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