Your deep dive into pond keeping is admirable, but you will find many, many, MANY opinions on ponds that are as different as night and day. I got the boot from several pond forums when I first started out because I had (GASP!) rocks in my pond! In the eyes of many, that's a surefire way to kill all your fish and probably yourself, too. They told me my pond was too dangerous for me to get in, let alone keep fish - all the trapped debris would rot and turn into toxic waste apparently. They also scoffed at my bog filter - said my water would never be clear and my fish would all be dead in a matter of months. (Spoiler alert - neither was true.) Even faced with the FACT that my pond was functioning beautifully after one, two, five years, they continued with their dire warnings until they finally kicked me out. And every single "fact" they stated was backed with "research" and "studies" and decades of pond keeping "wisdom". They could not accept that you could keep a pond full of fish without constantly tinkering with the chemistry and testing constantly and cleaning complex filters and backwashing and water changing and adding salt and on and on and on. Meanwhile, I was just hanging out, enjoying my pond.
One important question - what kind of pond do you want? If you want a garden eco-style pond, then that's the direction you go. If you want a DKP (Dedicated Koi Pond) then koiphen are your people. The reason they have to be constantly vigilant about water quality and fish health is because they purposely overstock their ponds. They want to be able to keep as many fish as they can in their ponds, so they push the limits. They compensate for their overstocking by using filtering systems that rival anything NASA has built. Some of them have whole garages full of filtration. It's pretty impressive actually. But what you won't find in a DKP is rocks, gravel or plants... which are all vital to an eco-system pond.
The moral of the story is - you will always find someone with a "better way". (Usually they're trying to sell you something.) For myself, in our quest to build a stress free pond, we came across an old guy who had been building and maintaining ponds for decades. He shared one piece of advice that stuck with me - "fill your pond and leave it alone. It can take three years for pond water to mature. Once it does - treat it like gold."
You've gotten off to a rocky start - I get that. You want to protect the fish you have - also understandable. What they need most is a stable environment. One sure way to KEEP your water from cycling and to STOP that bacteria you're looking for from growing is to keep emptying and adding more water - not necessary. AT ALL. The only reason I would remove water from my pond would be if something toxic had gotten into the water. Other than that, removing the water is never the solution. Another way to mess with a new pond - keeping adding stuff. You want a natural pond? Then trust nature. You want to be continually stressing about the newest "problem" - keep tinkering.
Do your research in your backyard - stay off the Scholar. None of us here are that smart (well, I know for sure I'm not!) and yet here we are - happy pond owners!
You said you would have questions about plants later - my suggestion is you start asking THOSE questions now. Get that pond planted ASAP. Nothing will help stabilize your pond faster than some healthy growing plants.
