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The valve cover and below the distributor are common sources of leakage up top. The marks you see on the bottom could be from this oil running down to the bottom of the transmission, or it could be from road debris and crud.

I cleaned the case of my transmission and still could not get rid of the staining in the top layer of the metal. (ie: a form of anodizing had occured) I sandblasted the case and painted it with an aluminum coloured engine enamel.