Several years ago I had to bead blast a crankcase to remove the external 
corrosion that could not be chemically removed.  I protected all the oil 
passages - something I'm sure your local machine shop didn't do.  

In any event, I found a shop in California that was able to 
ultrasonically clean the crankcase for me.  I would recommend that you 
consider doing the same - have the case ultrasonically cleaned.  In 
addition, if they blasted the mating surfaces (almost a sure bet - as an 
appretice usually does the cleaning, you will need to have the case 
lapped and alignbored.  Make sure the shop has boring, not honing equipment.

Hope this helps.  If you can't find a local company that has a big enough
ultrasonic cleaner, let me know and I'll look up the address I sent my 
case off to.  As I recall, it was the only shop on the west coase I could 
located.

Fred