There are different issues here, but certainly using a travel agent in this case would have solved SO many problems.
I would never try to book airport transfers on Newark several days ahead of time - most of those New Jersey Car Services have trouble remembering a booking made one day in advance. The price is also the same whether you reserve the same day or the moment you arrive.
But the point is that having an extra set of eyes (a travel agent) would have eliminated almost all of your air and transportation problems. It also would have cleared up the due date on the balance of your cruise.
Yup, a textbook case for using a travel agent if ever I saw one.