Thanks for all the help! I think I'm almost good! The vaccuming to waste is really working. It's a slow process though because I lose so much water that I have to stop and refill my pool before I can vaccum the whole pool. I can't vaccum too fast or it stirs the stuff up but at the rate I'm going it is taking a lot of refilling. I've probably got 80% of it out. A couple of more vaccums and hopefully I'll have it.

Is the key to avoiding this mess again just to really make sure I don't get low on chlorine?

I did the chlorine overnight test and I didn't lose chlorine so I think it's just dead algae that I have to get out, my filter doesn't seem to trap it.