1.: take the scan with the missing feet and blow it up
2.: take a scan of the feet and blow it up, so it fits the other part of the artwork.
3.: lock both layers
4.: start at least one new layer
5.: take the 'pen' tool and start redrawing all the black stuff. outlines and such.
6.: start a new layer, put it between the scanned artwork and the one with the black lines and fill the colored spaces as close to the original as possible.
hard to describe in a foreign language, but what i meant is that a scanned image will most likely look crap, since you would see all the little colored dots (magenta, cyan & yellow) and stuff ... maybe even some kind of moiré ...
example :
matrimelee manual 720dpi scan @ 100% :
http://home.arcor.de/supergoose/neo_geo/matri_before.jpg
http://home.arcor.de/supergoose/neo_geo/matri_after.jpg
it's only a start so you can see what i meant. just imagina what a higher res and more blown up scan would look like ...