I'm going to respond to the last 3 at once here.
The mud was not just mud. It stunk so badly of rotten eggs it made me feel sick. Once it was disturbed, when I refilled the pond, I didn't want it to get in the water, so I vacuumed it all away.
The bog I didn't know wasn't actually working. When redoing the kitchen cabinets, I found the original owners pond book about their pond. While not completely informative, I did find out the bog should actually be like a second waterfall. It was barely a trickle. No visible water when looking at it. I did that freezing in the winter before starting up so I didn't kill the plants. I excavated through the 7 years of decay that had clogged it. Left the lowest portion alone because while slightly mucky, it was mostly just dirty looking water. That mud also did stink. Badly. I rinsed all of the pea gravel, cleaned the lava rocks. Made sure the bog didn't stink like that by disturbing the remaining stuff in quite a few spots and sniffing. Put it all back together while seeding it with cold weather bacteria right before I could turn the system back on. There was only one little spot I couldn't do because I ran out of cold weather. I didn't want to hurt the plants. I also found tons of dead root balls and bulbs that were just rotting. Now the plants have room to grow, and water is moving trough it to make a gentle waterfall. It's probably at 85%. I also found out there is a silt chimney, so I cleaned that out. This winter, I will clean that last section up. I did it per the design instructions in that pond book. I also found like 200 slugs and I think what was a bird or some other very small animal remains. Hiding in there. When I restored the pond, I cleaned, but because I didn't know very much about bogs other than not to mess with them unless you have to, and I didn't know very much about plants/thinning them, I only cleaned out what I could see on top. Thinking anything else would decompose and filter through. The water that comes out of the bog is crystal clear now too. I can fill a jar and leave it for a day and there is no sediment. So other than thinning the last plant group because it doesn't seem to be growing well compared to the others, I don't see needing to do anything else to the bog.
We only added a few fish last year. A few comets, shubunkins and 4 koi. Thinking that would be it. A raccoon got one of the koi. Injured another. Most of the comets disappeared over winter. I think the racoon got two of the shubunkins. They were too curious and would come right up to the edge if they saw something. So we only had 7 fish. 3 comets, 1 shubunkin, 3 koi coming out of winter.
This year we settled on 14 fish total. The pond held 17 koi for about 20 years for the original owner/builder. So we decided on a few less total and half goldfish. We now have 11. The less than forthcoming seller we had been using, said he quarantined them. It was more like 24 hrs. We now have a seller that actually does a minimum of two weeks depending on how relaxed the fish seem, and we will replace the fish that passed eventually. Bringing us to 14. Half koi, half goldfish.
I would have kept the new fish longer before adding them. They need 2 weeks post shipping before even exposing them to a pond. We trusted him, acclimated the fish to our pond and let them go. 1 died from infection that lead to kidney failure (dropsy), 1 from a fungus, 1 starved. I caught them each when I noticed them isolating. Neither lived longbenough to complete treatment. The one that wouldn't eat, ate nothing offered. The flukes had already been eradicated before adding new fish-this was a best guess but Praziquantel ended the flashing and darting.
Seeing a fungus in the pond had grown so much on the little one, sluggish/isolated behavior in a few others, and unable to catch most of the fish because they can dart into the rocks, we had to treat the pond. As they grow big enough to catch without killing them from stress in the chase, we will use a hospital tank. The comets are small and our shubunkin is stunted. The comets we got were practically fry still and the shubunkin hasn't grown in the past year. The fins have, but it looks like it should be in an aquarium. They're super fast. And have 40 places to hide or more.
My ph has gone above 9. Right now the only thing keeping it where it is, is baking soda. It's able to act as an acid or a base neutralizer, it was available and it's holding the line for a moment. But it is temporary. The ph rose to 9.5.
The reason for the coral plus cracked corn is to increase calcium and CO2. If the coral is sitting on the cracked corn, it will dissolve. I forgot in my notes it says to use powdered dolomite to bring levels of calcium and magnesium up first. Then longer-term, the source leeches into the water And is the coral chunks + limestone or dolomite chunks. I jotted that in the margins.
I haven't added any of those yet. Only baking soda and continuing with clay because the fish LOVE clay days. They getbright to foraging and don'teven bother coming for pellets until the evening feeding.
I'm trying to make the game plan and then execute it so I can get back to enjoying the pond. None of this works if the base of the ecosystem is broken. Hence wanting to seed good bacteria to boost it. The speed up is because I don't want my fish weak and susceptible to anything else. I also want them to have peace instead of me doing stuff all the time. I mean they don't scatter when skimming the top or bottom anymore. My neighbor has some massive evergreens and I get tons of debris every time the wind blows, so I have to use a fine net under the waterfall where it gets pushed to the bottom To get pine needles, pine cones, sometimes moss/fungus and even whole small branches when wind is high.
I do not want to use gypsum. The article makes that sound like a bad idea.
I hope that answered or helped elaborating.
I also woke up to a 2" water level drop, so now I have to chase water loss. I swear Murphy is staying at my house making sure their law is upheld. Fingers crossed it's just in the waterfall.