OK. The boat is 3 hours north and we went up this past weekend. I had a fuel pressure tester and a new fuel pump just in case. For reference, AutoZone will sell you a very nice fuel pressure tester (with the t-fitting if you do not have a schrader valve on the fuel rail), and your money is refunded after returning the tester.
I installed the new alternator (which seemed to have a larger pulley on it because the belt was extremely tight), and went looking for the key. After having to hot-wire the boat since the key was 3 hours south, it fired right up. The boat ran perfect all weekend for a family reunion, and the surging and cutting-out of the injectors were the result of a failing alternator. This seems strange since the boat battery never failed to charge and start the boat (until it finally failed a few weeks ago).
Anyway, thank you for all who posted and a special thanks to JimN who traded numerous emails with me when the problem first started.