A year or so before UE was finished, I asked KillerWave to get the science vessel working (the plan being to have such a ship hanging around Beaufort, just for variety's sake). However, this turned out to be practically impossible - there's something screwy in its mesh, and there was always a lot of collision-related problems (although it was functional enough to work as a cutscene-only ship).
Anyway, I'd be quite willing to provide you with the version that KW made for me if you PM me with your email address. But the only way to get the science vessel properly working, IMO, would be to make the model from scratch, using the current version as reference.
BTW, you do not need to add a ship to ship.iff in order to use it. This file exists for two purposes - first, to define which ship gets which VDU, and second, to allow you to spawn ships. If you don't mind your ship not getting the correct VDU (and this is seldom an important issue when you're just testing stuff), and you don't need to spawn it (which is also generally not necessary when you're just testing stuff), then you do not need to touch ship.iff. Furthermore, ship.iff only includes ordinary ships - it does not include capships. So, if you're working on a capship (as is the case here), you can forget about ship.iff altogether.