Tsukihime's map connection script will not help you reduce lag. The game renders the small connected maps the same as it would render a large map. Since your map is so drastically segmented (visually) why not make it into three separate maps? One for the green area, one for the sea, and one for the gray area. Since you say the player is using a ship to traverse the sea, I guess there must be a "step on the ship" event, right? You can make it so that the green map ends where the player finds the ship. Then when the player enters the ship, they'll be taken to the sea map, but the start of the map will looks just the same as the end of the previous map, so it gives the impression that it's still the same place. The sea map will end where you land on the grey map. And the grey map will begin where you land the ship. The only transistions would be present when you step in or out of the ship. I don't think the player will mind a flash or fade out/fade in transition for that.
Autotiles cannot scroll like parallaxes. But there are some animated autotiles for water that are good enough to map a sea.
The demo for Galv's layers script included a part where he simulates water by overlaying 2 images and setting them to scroll in different directions instead of using frames. His demo doesn't really suffer from lag, but his sample maps are pretty small compared to yours, and he isn't using frame-by frame parallaxes.
From what I have seen, anti-lag scripts keeps events from updating if the player can't see them. A few also prevent some lag with sprites and animations. I haven't seen any that are made specifically for events with large graphics. I'm not really sure, but lag from events seems to come more from the amound of events in map and the amount of processes the game has to handle because of them.
Maybe you will have to make smaller maps, use less parallaxes, or limit the use of parallaxes to smaller maps.