I think what you'll want to do is Group the spaceship to... itself!

So, you'd have Group A containing Group B. Group B would be all of the ship's compenents themselves.

By attaching Group A to the motion path, it leaves Group B alone, and you're able to animate the rotation of Group B independant from the motion path...

I hope that makes sense.

As for landing pad animations, I think I would go about it by using set driven key animations attached to a Locator. I've got a little tutorial going over that kind of thing. It's at my site. Link in the sig.

Just parent the locator to your group and it should be all set.