To get everything the same size is a fairly 
painless problem. My solution was to figure out 
the ratio I wanted for height and width and make 
a blank photoshop document. I added a frame 
around the whole thing 1 pixel black, 1 pixel 
white. This frame is always the top layer. Once I 
have cleaned up my scanned image, I copy/paste it 
into the frame set. Then use edit>transform>scale 
to resize it. The shift key will make sure 
resizing remains proportional. When I'm satisfied 
I use "save for web." Repeat for each cel, each 
comes out the same size with the same border. Odd 
sized cels get a little extra but thats about it.