How to line up the pieces at the coast near the shipwreck

There's a possible interaction between your numbers 1 and 2 that you're missing. The blue blocks only subtract from yellow blocks that are in the same space. Let's work with an example 2 box puzzle. If there's one blue block in one box, and a yellow block in the other, the solution is to go around the edge of the puzzle, not to go through the middle, splitting them up. If you cordon off the blue block from the yellow block, then the blue block doesn't do its thing, so it's not a valid puzzle solution.

So, be sure that you design a solution that has all the blue blocks in the same space as yellow blocks.

And yes, this is a super tough puzzle, it took me quite a bit of fiddling to get everything in place.

As you requested in the comments, here's a quick solution. Took me less time this time around, since I vaguely recalled some of the tricks I used in the solution.

@Devon Parsons answered quite correctly, but to make the answer more complete:

1. The pond is a very clever map of the whole island. All parts of the lake facе to the corresponding areas. The lake's water corresponds to island's shore; and the wet shore (rocks) near the lake correspond to island's water in-between shore (where tree houses and shipwreck is located); actually you can see the shipwreck in the lake as a piece of metal; also you can see a woman statue, which correspond to the statue on the mountain.
2. 11 big lanterns are the lasers. If a lantern lit - the laser is activated.
3. 6 fountains are the obelisks. If a fountain is high in the air - all puzzles on the obelisk have been solved.
4. The flowers are the audio-logs. White flowers are the usual ones, yellow - are the golden, which you can find underground when open the mountain secret door. If a flower blossoms - the log were found and activated.
5. 7 clams are the vaults with sheet of paper inside. If a clam is open - the vault was open.
6. Finally and most importantly for the completion: 14 triangular leaves are the small 3x3 puzzles scattered around the whole island. If a leaf is sunken and hardly visible - the puzzle was solved.
7. Unfortunately, the lake doesn't label "usual" puzzles, to be sure that you've done them all you need to go to menu/saved games and check the first number to be 523 (the second and third correspond to the puzzles on the obelisks and number of the obelisks, they must be +135 +6, but you can check all of them with the lake and the obelisks themselves). Some of those "usual" puzzles are tricky to find, but most of them you won't be able to avoid when you will hunt for the listed above lake-things, the rest easy-to-miss-puzzles are the ones, which allows to use various shortcuts and shortcuts (these shortcuts should be relatively obvious). Once you've done all of these you should have 523 puzzles count, but if you stack you can use this manual, for example.