I am trying to combine images scanned from microfilm in the case where the
lens on the microfilm scanner is too powerful to permit me to scan an entire
page into a single image file.  I believe that this application is similar
to trying to create a landscape from multiple photographs.

I scan the original into a PDF containing multiple images.  I then open this
PDF as layers.  I have been able to rearrange the layers, raise and lower
them, and merge them to create a single image file, but I have 2 problems:

1) Sometime the key spots within the layers which I need to line up prior to
merging the layers are not right on the edge of either layer.  To perform
the alignment I need to make at least the outer portion of the upper layer
partially transparent so I can properly align them.
2) Once I am finished the contrast between the two layers is generally such
that the edge of the upper layer is clearly visible in the merged result. 
Once again if I could make the outer edge of the upper layer transparent on
a gradient to fully transparent at the edge, I could make the edge
invisible.  I think of this operation as "feathering" the layer, but
searching through the documentation and web guides I can only find
"feathering" as applicable to images, not layers.

The following is an example of the result I currently have:

http://www.jamescobban.net/Ontario/images/B1912_33007.jpg Combined image
from microfilm. 
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