Why does the Jones act discourage trade between PR and the Caribbean? My understanding is it mandates use of US ships for shipping between US ports. It should therefore have no effect on shipping between PR and the various non-US Caribbean nations.
The act says that anytime a non-US ship carries goods that are from a US port, including Puerto Rico, it cannot take those goods to any other US port. So instead of being able to do a sequence of [Barbados, Puerto Rico, Florida, Barbados], a ship would have to instead follow [Barbados, Puerto Rico, Barbados, Florida, Barbados]. It doesn't eliminate trade entirely, but it definitely increases costs--especially in PR itself, which has to rely only on US ships for US goods, creating a monopoly.
I don't think the US would stop trading with Puerto Rico, so I suppose the question is if the increased trade with Caribbean nations would offset however much trade with the US mainland would diminish. I don't know the answer to that, but it could probably be found by looking at how Caribbean nations' trade compares with Puerto Rico's trade today.
Yes, I'd just expect the "common market" effect would be significant. I'll bet it would have been harder to manufacture pharmaceuticals for sale in the US in the Dominican Republic, for instance.