There might still be leftovers from the previous failed compilation.
To fix this:
cd $NWCHEM_TOP/src/tools
rm -rf build install
make
Another possible problem (from your error log) is that the gfortran you are using is not compatible with your assembler (suffix or operands invalid for `movq'), but I cannot help you on this one. An option might be to using Mac Brew instead of Ports