just a geuss here, but pesticide or weed killers in the lawn could have got on/in the pump, like otheres here suggested. cleanning it with vinagar might have done some good. whatever it was your doing the right things now with heavey skimming, carbon and water changes. i also agree with adding O2, if nothing else a couple airstones to help out and increased flow, esp at the surface. hope things start to look better soon, keep us posted.
o, though its likey the pump at the root of the problem, have you tested your RO/DI water for chlorines?