I get the big performance hits with the Galiur Shuranis or whichever it is, the expensive one.
I haven't tried the Stutter Remover, I may have to give that a check. Thing of it is, my computer is only a couple months old, with pretty good stuff in it. I should get FPS lag on any game I play at the moment. I've got an Nvidia Geforce 9800GT, 4 gigs of RAM, I shouldn't really have any problems lol.
I was getting a crash every half hour or so with my other mods active. With only the sailing ships mod going, I didn't crash, but my FPS still took a hit :\
I did notice a couple other things. When I traveled a bit too far south and hit the Valenwood border, my ship kept on going while I got tossed off the back. Not a big deal, I was actually looking to see if that would happen. Unfortunately when I loaded my save (it was an autosave actually, from when I went below deck) I found myself at the bottom of the ocean with no ship in sight. Moral of the story - don't load a save from inside your ship while at sea. That seems to cause a problem.
Also, the Stohrker (I know I have these names so totally wrong that it's not funny, but I think you should be able to deduce which ones I'm talking about) has a problem with the stairs. I tried to climb the stairs, and first of all you can't mount them without jumping. My character got stuck at the bottom and I had to jump onto them. Second, I fell through them. Twice. I had to fast-travel to get un-stuck, with the wooden planks of the stairs running through my chest. I did manage to get around them though, by running up the solid piece along the side.
I figured out what caused me to get stuck the first time I took my ship out. It was the Galiur Shuranis that I got stuck in, there's a little dinghy at the end of the dock and if you turn too soon you "run aground" and can't move anywhere, because your ship gets stuck in it. That's not really a problem, just an inconvenience.
Also, like someone else said, the elven ships with the little roofs. You get put on top of them. A lot. And if I may say, the Galiur Shuranis is hard to mount right out of the dock without a high acrobatic skill. I had to jump on one of the pylons and then onto the deck, otherwise I could only get on by activating it while swimming.
Can't wait to see the interiors of the other ships for sure

And I'm curious, how will you get anywhere by having a first mate steer the ship? The only place to go is Anvil, nowhere else is accessible by water. At least not in ships the size of these.