Well, after becoming pretty sure that I've removed all the breadcrumbs from having the compiler installed under /usr/local, I tried the process again, now it can't find any of the headers due to looking for them in /usr/local. Heres the new include search paths.
Code:
ignoring nonexistent directory "/usr/local/lib/../powerpc-wrs-vxworks/include/c++/4.8.0"
ignoring nonexistent directory "/usr/local/lib/../powerpc-wrs-vxworks/include/c++/4.8.0/powerpc-wrs-vxworks"
ignoring nonexistent directory "/usr/local/lib/../powerpc-wrs-vxworks/include/c++/4.8.0/backward"
ignoring nonexistent directory "/usr/local/lib/gcc/powerpc-wrs-vxworks/4.8.0/include"
ignoring nonexistent directory "/usr/local/lib/gcc/powerpc-wrs-vxworks/4.8.0/include-fixed"
ignoring nonexistent directory "/usr/local/lib/../powerpc-wrs-vxworks/sys-include"
ignoring nonexistent directory "/usr/local/lib/../powerpc-wrs-vxworks/include"
EDIT: Fixed this. I had old binaries in /usr/local/bin that were causing GCC to think that it was installed there.
EDIT 2: Only problem I'm having at the moment is cpack putting wpilib in the wrong spot. I'm trying to use cpack just to learn how to before reverting back to the regular packages. cpack seems to ignore CMAKE_INSTALL_PREFIX.