I found the best way to really clean a sandcast motor is to remove it from frame (or at least strip as much as possible in the frame), plug the intake and exhaust ports w/ plastic milk bottle caps, then drown it in EZ-OFF oven cleaner (wear HD rubber gloves and eye protection), flip it upside down on a wood beer pallette, scrub w/ toothbrush, scotchbrite, hose it down, then etch it w/ hydroflouric acid (wire wheel/chrome cleaner). All engine covers will need refinishing (I like polished aluminum ceramic coated); the crankcases will now be super-sanitary.
These iconic motors should look tough and rough; not pretty.