With further research, I've discovered that for the purposes of the Jones Act, Puerto Rico and the Virgin Islands are not considered U.S. ports. (yes, I know that Puerto Rico and the Virgin Islands are a part of the U.S. - but not for purposes of the Act). According to Royal Caribbean, I can take a round trip cruise from a U.S. port and leave the cruise at any point along the way. To do so requires the permission of the ships Captain, in advance by fax. This only works on cruises involving Puerto Rico and the Virgin Islands when sailing from mainland U.S. ports. It will not work for the west coast for cruises to Alaska, Hawaii, etc.
I've checked with other cruise lines as well, and they all permit it, bearing in mind that you have to pay the full cost of the cruise. The trick is finding a cruise where the Puerto Rico stop is later in the cruise, so you can at least get some enjoyment of the other ports along the way and get you monies worth.
One of the cruise lines (don't remember which) called what I want to do as "Down lining".