Well, the way I'd go about it is to first get the animation to look right. Then expand the canvas by 1 pixel on all sides. Put a 1-pixel thick border around it (separate layer), create a new file the same size as a single frame (including border), expand it horizontally to fit all the frames you'll have, select all, CTRL+Shift+C to copy the visible image, and paste it into the new file. Place the frames side-by-side. The borders will ensure that they're aligned as intended. Finally, flatten it and delete the borders.