It came with its own gromets....do I use the metal inserts as well that I took off with the gromets or just the gromets themselves

Remove the metal inserts, clean and re-install them with the new grommets.
I just did this on mine a few weeks ago.

If you are missing some of those metal inserts, where could I find them? Rockauto didn't seem to have them...

I lost one during the install and fabricated a new one using a 5/16" T-nut from the hardware store. Just measure the length (file and/or grind as required) to ensure it's the same length as the OEM originals. That way the gasket crush will be same all the way around after torquing the cover bolts.