I think a three way valve might be worth adding.

The filter is clogging with live algae I assume. When I pull it out and wash it off the water is almost completely green. I was leaving for a two week vacation and needed advice.

I pulled the filters out and ran the pump, everything worked just fine. The pump is now running while we are away sans filter and I will have to deal with it when we return. It has become quite the frustrating mess unfortunately.