NEVER use DV or HDV for stop motion, never, you adding interlacing and throwing away of color info.
Use ProRes (progressive) and a video resolution 1920×1080 is the top. The frame rate is determined by the look you want, 24 or 30p.
If you are taking still with the camera the video settings never come into play.
One thing I would recommend is using Motion vs FCP to put this together. Since the shoots are sequential Motion can bring them in as a single file, does better with adding pans and zooms. Just a suggestion, if you want to type it out.