I think that is a fairly common swap, but you will need to make new mounts for the engine and tranny on the SJ410 frame. You might also need a small body lift or a Samurai hood to clear the engine.
I've read that the SJ410 carbs were actually pretty good, better than the Aisin or Hitachi carbs on the 1300 engine. Although, I have no personal experience with them. I seem to recall that the SJ410 carb was a sidedraft carb. Take a picture of what you have and post it please.