Sam,
I am suspicious that something is already wrong when you run ungrib. The gfs file may not be successfully ungribbed.
Please download GFS data at the websites: https://rda.ucar.edu/datasets/ds084.1/
remember the keep the filename as is in the website and don't change it.
Then you should use Vtable.GFS to unngrib the GFS file. Please start with just a single file, run ungrib and metgrid to process the file.
I suppose that you should be able to produce met_em file. if not, please save all the log files for me to take a look.