Hard to follow exactly where you're going with it from the videos but one suggestion that I'd make before you get too much farther... Get the liner up higher at the rim of the pond so that it's above ground level. Otherwise, you'll have runoff going into the pond. Usually what I'll do is to lay my worst/scrap rock around the edge on top of the liner and then fold the liner back over that layer. Then finish with better rock however on top of that. That gives you several inches of height as a buffer and lets you raise the height of water in the pond a little higher so that it blends into your rock work better vs sitting down below it.
Also, make an overflow where you want excess water to go in a directed way vs just randomly flooding out where you might not want it.
A bottom drain is a good idea but probably too late for that and may not work with the soil.
Build in a skimmer. Makes a big difference in keeping the surface clear and helps filter out a lot of what falls/blows in.
San Fran likely will be too cool for a lot of tropicals. Also, smaller fish that aren't very brightly colored you'll pretty much never see.
Ponds aren't just bigger aquariums. You need to take a kind of different approach to them.