Just watched most of your pond build videos in my free time over the last few days. Big project and looks awesome! I really liked the negative waterfall leading to the large water revisor basin. I hadn't really seen this type of setup before and found it interesting.
Read the last few posts here and had some free feedback (of course it's worth what you paid), but maybe you will find it useful??
I know you talked about adjusting PH levels, but as an owner of a pond with 8+ PH it's a losing battle long term. It always seems to bounce back and I've read it's best to just leave it stable and higher than trying to fight it. I've found this to be true in my personal experience as well with no ill effects that I can see.
I've had a lot of luck adding salt to the pond. I use swimming pool salt from a hardware store. I found this is the most cost effective way to buy it. It has helped knock out a snail population, parasites (might help with your duck mites), and when dumped on string algae wipes it out so it might even help with that issue. The salt also doesn't appear to affect my goldfish or plants negatively.
My goldfish keep the string algae from getting too long as they are constantly snacking on it so I don't hate the idea of adding them to help with that. If you are concerned with the bio load increasing ammonia levels it might be worth looking into a gravity pond filter setup. It could be hidden under your deck and used to feed your stream coming out from under your deck. I know everyone pushes bog filters, but dedicated pond filters work really well and are cheap to DYI. Just something to consider if you hadn't already.
I've found that with the pond plants (including water lilies) if they aren't doing great to raise them up in the water column. Most pond plants are weeds and grow like crazy so if they aren't doing much it means they are very unhappy. I've found even changing the water depth by only 1-2" can have a big impact on growth rates. I found that water depth impacted my water lily pad grown more than fertilizer. However, if you want a lot of flowers on them, they do need the fertilizer. Sun is a huge factor as well, but there is likely not much you can do about that.
Late to the party with some of these replies on a few of these topics. You might have solved a lot of this already. Others may have had different results, but with luck you might find some of the above helpful!