I argree with Greenman - that's a pretty good result. You could probably get a better result if you moved the seam away from the gutter (assuming you have the space) but it's probably not worth it unless you're prepared to pull the magazine apart.
On the other hand I think you're overestimating the difficulty of alignment. As an example here's "one I did earlier" (Aways wanted to say that.)
http://img210.imagevenue.com/img.php..._123_550lo.jpg
The only alignment I used was to make sure the top of each page was flush against the scanner frame - mine has a lip but a ruler taped in place should work as well. There's a few pixels variation in the original scan but you'd be hard-pressed to see it in the final image.