Eric, I think you got some excellent advice on this thread and this would apply to anyone that is thinking of cleaning a pond on the proper do's and don'ts. I don't understand that if you now realize your fish are probably in crisis mode because they are swimming in their own waste because there is little good bacteria left in the pond to absorb it, why would you buy additional fish that will produce more waste until your problem is completely resolved?
1) Filter. May I suggest again the pre-filter that I posted previously? You can add that in place of the intake you have. Alternatively, you can put some filter material in the cage you have. Ask your store to see what they have. This is for filtering solids. For a bio-filter, you already have a long waterfall. I'd just add gravel there. A lot/some people might disagree on that, so that's just me wanting a natural bio-filter to go with what you have.
2) Don't add any more fish for now. More fish means more waste products.
3) The green is fine, it's algae and they will help get rid of the waste products. The pre-filter will get rid of it, at least in my pond it does.
4) 50% is a lot, imagine changing 50% of your environment. Do smaller changes, I'd do 30% max.
Something similar happened to my koi fish this weekend,I pulled out all the plants around the pond especially the crawling plants on the side around the pond,I did not changed the water,but my koi fish are very skittish and refused to eat their foods,they are hiding in the bottom,they refused to come out when they see anybody coming close to the pond, I dont know what is causing this behavior,I hope they dont die from starvation