The inspector came yesterday and signed off on everything except the new metal boxes we put on the ceiling for lights. He said they should be grounded... We've prepped the wiring (consolidated ground wires from the Romex), but how do we "ground" the boxes? Do we do this by just connecting the Romex ground wires to the boxes or is there something more..

With all the grounds spliced, there should be one additional "pigtail", a short piece of wire twisted under the wire nut at one end, and the other connected to the metal box, using a green machine screw threaded into a threaded hole on the back of the box.

You can either just get green screws and use your own wire, or there is ground pigtails all made up with the screw and the short piece of wire.