Warping in:
One way is to place the ship at (0, 0, 0) and then give it orders to warp in at a certain time (like 00:05). Then set up a sexp which uses SCP variables to display the current coordinates of the ship when you press a key. Then fire up the mission, wait for the ship to warp in, wait for the ship to come to a stop, and read off the coordinates.

This way would measure from center-to-center, so you if you wanted to measure the distance from warp-effect-to-center, you'd have to subtract off the length of the ship from the center to the front (which may not be equal to half the length of the ship). The easiest way to do that would be to place the ship so that its front is at (0, 0, 0), but you'd probably have to eyeball that.
Warping out:
Not sure about this yet. The best idea would probably be to measure the distance from the center (or front) of the ship to the point at which the warp effect appears, but I'm not sure how you'd get the coordinates of the warp effect.
Of course, the best way to figure this out would be to look it up in the source code. But I'm a little too busy/lazy/occupied-with-other-priorities to do that at the moment.
