mark, when it done it will look like this so you can either crop it, warp it, or clone in the areas that are missing. Its best when shooting for panoramas just to take a few extra outside the are you actually want to allow photoshop to fill in these gaps so you can crop back to what you actually wanted. You can see in this one the effects of not having the camera in manual.
http://www.flickr.com/photos/41963775@N07/3987838669/