Ryan,
As you noted the paths are broken because the Path variable that those files are relative to, is not properly maintained during the export/import process.
I believe what you are running into, unfortunately, is a known Eclipse bug. Due to the bug, the File Export/Import method of sharing projects is not recommended in CCSv5. Please see this thread starting with this post: http://e2e.ti.com/support/development_tools/code_composer_studio/f/81/p/265436/928418.aspx#928418