At this point I consider the mod to be mostly feature-complete. I'll put the full details in the opening post, but the gist is that I've modified the Lighthouse and the Seaport slightly. I decided to leave the Harbor and Shipyard alone. The building changes are in separate files, so you can remove both of the files that have "building" in the name to remove those changes if you want to use this mod in conjunction with another mod that modifies the harbor and its buildings.
I'd appreciate feedback re: Naval Tradition. This is the civic that feels "right" to me for the fishing boat adjacency boost, but the AI tends to ignore it, which hurts them. If I moved it to a civic like Civil Service or Guilds, the AI would be more likely to utilize the Medieval adjacency boost. Thoughts?
Also, make sure to tell me if you encounter any bugs or weird behavior. I haven't found any in the game I'm running to test the mod, but feedback is always helpful. One thing: this mod will only affect buildings that have been built since the mod was updated. If, by chance, you were using a previous version of the mod and built lighthouses or seaports and update to this version, only newly-built buildings will be affected.
Here's a screenshot of a post-Plastics Islands map with lots of fishing boats out: