We will be deboarding a cruise in Rome this summer and are spending an extra night in Rome to enjoy some of the sights. We will probably get off the ship mid morning. I was told to take a shuttle or limo service to our apt, since this method would be faster than a train. However, the apt has told me they cannot store the luggage for us until we check in which would be at 4pm. Does the train station have storage facilities for this purpose? We will most likely have two very large suitcases with us. If so, would we have to take the train from the port to take advantage of the storage facilities? Thanks for your help.

The port for Roma is Civitavecchia which is about an hour from Roma by train.
Roma Termini, like all main Italian stations, has a manual left-luggage office.

Does a "manual left luggage office" mean that we can leave the suitcases there for several hours or is this more for lost bags left on trains?

The manual left luggage means you check your luggage (not luggage lockers). Here's the link for the rates.
http://www.grandistazioni.it/cms/v/i...003f16f90aRCRD

I would train from Civitavecchia to Roma Termini. Check the luggage at Termini. Hop on the metro to the Coloseum (only 2 metro stops from Termini) or hop on the other metro line (there are only two lines - A and B) to the Vatican depending on which you want to see. Termini is the main change station between the metro lines. Ticket machines are downstairs by the entrance to the metro.

Thank you so much, KyBourbon. I think you've helped me out before. That's just one more little detail that I can check off the list! And yes, the Coloseum will be our first stop.