Pool disaster...how do I make it safe again?

Returned from 2-week vacation, discovered pool filter stopped working during trip (probably shortly after I left given the mess). (Above ground, 12' x 20' easyset...saltwater chlorine generator system). Green water, some floating goo (and two dead birds), lots of mosquito larve, and bottom covered with layer of sediment. Fixed filter and let it run for 48 hours with the generator also running. Skimmed off gunk with regular pole skimmer. Water returned to clear and all the mosquito larve disappeared (found then caked in the filter cartridge) but sediment remained...when I vacuumed it with filter vac attachment I noticed that there were several kinds of "kritters" still living in it ...mostly some thin red worms (kite string sized abt. 1/4 inch long) and some white/clear things that looked like little shrimp! Now after one week, I'm still finding the red worms (alive still)...is it safe to swim yet...should I drain and start over...do I need to shock it on top of generated chlorine