Regarding your cases, they can always benefit from a little cleanup of the casting marks. Just use a rotary tool with a sanding drum small enough to get in there and smooth all the rough edges. Don't try to take that stuff off on the one side that looks funny, just get the rough edges smooth. Porting is not about making the holes bigger, it's about helping the air/fuel mixture flow quicker through the system. Those rough casting spots only slow the air down so taking them off is ok. Don't get too crazy.

Once your done clean them, then clean them a few more times. The best method is in a big sink with hot water and dawn dish soap. Scrub every surface and use little bottle brushes to get into all the journals. The vapor blasting that was done left residual material that you gotta clean out, plus any bits left behind if you do clean up the ports. If you did not remove the upper and lower needle bearings where the clutch throw arm passes through, you gotta pay extra attention in there. Spray a fair amount of carb cleaner in there. Once your done cleaning put a little 2T oil on them with a q-tip.