Hi Joel,
Please do not take this the wrong way, but your install looks too new for the reality of what is going to happen, to happen. You have 6 months to a year before you have problems. You will have waste that settles into the rocks. The waste will build up and become anaerobic, it will produce some dealdly gases and it will be a haven for parasites. Even removing the rocks every year and cleaning out the pond will be unhealthy for the Koi. It is inevitable.
A mud pond is nothing like your pond. Mud ponds are prepared every year by the breeders for their Koi. The Koi also only live in the muds for about five months at a time as well. I think that you would find that the Koi would have many problems if the breeders left them in the mud ponds for years on end.
I dont know what your seven stage filter sytem is but it looks as if the water is pumped from the pond to the waterfall / stream and back to the pond again. Please let me know if this is incorrect. Do you have TPR's for circulation, do you have a bottom drain, do you have a skimmer and where is your air pump for oxygenating the pond?
Your pond volume looks to be about 2000 gallons. Did you use a water meter?
You have a very nice looking water garden pond with Koi in it.