Sansebastian,

By the way, I am backflushing a lot of the stinky green solids out of the filter every other day. I hope this does not slow down the process of developing healthy bacteria. Any thoughts on this?
The green stuff could be you koi poop or sludge which must be removed for better water quality, IMHO

90% of the pond receives full sun. There is a small portion that is shaded throughout the day. My fish love that spot until I come home and feed them.
You may have to add a bit more shade to control your algae probs

It will be easy to cut the amount I feed them down if that will improve the water quality and the health of my fish. I have not checked the water levels for a week or so. I'll take a reading tomorrow.
Take it easy with the food, too much will give you ammonia spike coz your filter is still new and no beneficial bacteria to process the waste. And if I were you I'll check the water parameters asap.

I check the clarity of the water daily and am delighted to see that things are clearing up. I guess it will take some time before the system is actually set and stable. In the meantime, I'll sit back and relax knowing that I am slowly getting the right track.
The system takes a while to fully mature, once you're there its all a matter of good maintenence like regular flashing of filters, checking water parameters, etc. What your koi behavior, they'll be the first one to tell you that you have water quality issues

rgds,
Jon