Here is one suggestion: to clean the Top layer scans.
If you have the original scans…
Open Illustrator (or Corel Draw has a good tracing program as well).
Set the page size to match your animation layout.
Place the 1st scanned image.
Live Trace (use a good setting that captures all of the drawing and deletes the original).
Expand the trace.
Ungroup the trace.
Delete all backgrounds.
Export file as Transparent PNG.(name_1.png)
You can save this Ilustrator file or use it again. (see below)
Create a new layer.
Import next scanned page and place where it is required for the animation.
Live Trace (use a good setting that captures all of the drawing and deletes the original).
Expand the trace.
Ungroup the trace.
Delete all backgrounds.
Hide the previous layer.
Export file as Transparent PNG. (name_#+1.png)
You can save this Ilustrator file or use it again.
Once complete… in AE
Import the bottom background layer.
Import the new pngs as an animation. Mode as overlay.
Use curves, saturation, and other color tools to adjust the look.
It should match close.
Added benifit to this long process, the images in illustator are editable. Minor adjustments can be made and the image reexported as needed.
Others will chime in… with more experience… I hope.
Rob
Rob Dahl
Transparent Alchemy
Boulder City, NV 89005
http://www.transparentalchemy.com