When I was doing my Raiha-sequence animation, I 
tried to keep the registration holes of the cel 
over the dents in the background, and put pieces 
of tape on the edge of my scanner to help guide 
me. I still had some wobbling, but I'm sure if I 
played with it enough, I would have been able to 
get a steady animation. One of the things I 
noticed was that some scans turn out naturally 
lighter than other scans, so in addition to 
keeping an eye on the wobbles, you'll want to 
keep an eye on what color the bg and cels scan 
each time through.