Well, I don't know that outboard but I believe that you're going to find that the charging system has nothing to do with the ignition. So, I'm guessing that you are probably correct that the polarity reversal may have damaged the CDI as well as charging system components.
But before throwing parts at it you should go through the troubleshooting steps in the shop manual for no spark because the current may have damaged the exciter coil or even the pulsar coil and not the CDI.
The rectifier is fuse protected I believe. Have you checked that?
If the fuse blew in time, you might have caught a break there.
If you get it running you can then see if it will charge.
Good luck.