I've used glass beads, and have had an engine blasted with PLASTIC media. The glass beads, as was mentioned before, get into the tiniest of all places, and will clog up threaded holes and the like. It will also distort aluminum if allowed to contact a small area for too long. The plastic media is non abrasive, but the clean up is still a pain. It won't harm aluminum in any way, and cleans extremely well. After you have something blasted, either with glass beads, sand plastic, soda, etc. I would recomment having the cases professionally cleaned in a dip tank and pressure washed afterwards to clean out all of the tapped holes and oil passages. Maybe ultrasonic cleaning would work.
Just curious, but you mentioned that you were using case halves from two different engines? How is this possible unless you plan on having the case main bores re-bored so they match up?
regards,