Of course the best way is the hardest way. The only sure way to get it all out is to split the cases. But if thats not in the cards do this.
Go to Wal-Mart and get a gallon of mineral spirits. Should cost you less than $5. Fill up the crankcase and let the aluminum float to the top. Do it a few times. Work the crank around and make sure you get all the particles out. Make sure you drain all the mineral spirits out before you reassemble.
to check the cylinder..use a micrometer, they have em at most tool places..or take it to a local shop and have em mic it to see..or , some pistons are marked..look for numbers on it