How do I properly wash bugs out of green onion?
I'd cut the root off (so you have a green onion 'straw') and run water through that. This would leave the onion soggy. At this point I would lay out some paper towels at the bottom of a vase and leave the green onions upright for about an hour - switching the paper towels every 20 minutes if they get too damp. After said hour, store in a cool place. 

Do note that by cutting the roots of the green onion you considerably shorten their lifespan in storage. However, you can then take the roots and plant them (after soaking the roots in 1/4 water-to-root-height ratio) to get more green onions :)