Is it possible that your captain does not know how the batteries are supposed to be configured (and the wiring) and that he did something wrong while installing the batteries and trying to get it to work? Is it possible that your Captain performed the auto configure for the port engine incorrectly? It seems like it's pretty easy to know that the corroded case for the ECM is the case only and that if you want a new enclosure, you can buy one. Did you instruct them to replace the enclosure for the ECM when they replaced the ECM? This just seems like better communication is needed. It does sound like you are trying to save some bucks by doing some of your own work but possibly in the process causing further problems.