Like I said yesterday, I don't know if it's faster to do the bat caves puzzle, at the same time you set up the astrolabe, or if it's faster to get the beacon, at the same time you visit Half Moon Reef (therefore, putting off the bat caves until later). I'm presuming you do.
I'll just have to time it. Let's see. The first route requires you to get the beacon, right after underwater Sudoku. So the timing would be "underwater Sudoku to the beacon, to the dock", as opposed to "underwater Sudoku to the dock". The second route requires you to do the bat caves, after getting glowsticks from Johnny. So the timing would be "Johnny to the bat caves, to Blue Hole", as opposed to "Johnny to Blue Hole".
I'm going to presume that the first route is faster. So, once you get the astrolabe and the beacon, you want to do Coucou's perch puzzle. You also want to visit Blue Hole and dive there, to see that it's dark, to trigger Johnny's underwater glowstick puzzle. Hey, wouldn't it be spiffy if the correct Coucou perch was at Blue Hole? That way, you only have to take one trip?
And this is another place where I'd just have to time it. I guess the two options are...
1. Perch is at the first beach. You have to go from the resort, to the first beach, back to resort, to Blue Hole, to Johnny.
2. Perch is at Blue Hole. You have to go from the resort, to Blue Hole, back to resort, to Johnny.
Of course, the location of the correct perch could be randomized, in which case, you just have to hope that the random number generator likes you, and the first perch you grab is the correct one. I have no idea I saving/reloading helps with this puzzle. Another thing to check!