Open Your Paths First
It may be tempting to try and get all of the Stray Fairies in the dungeon without backtracking. However, it is far quicker to open up the pathway between the second floor and the first floor before actively looking for Stray Fairies. This has a couple benefits. One, if you get knocked off of the second floor accidentally, you won’t have to spend time running back through the dungeon to get back to where you were. Two, if you’re at the point where you can press the switch to materialize the ladders in the main room, you can also purify the water by lighting the torch on the middle of the wooden flower structure. This will make exploring considerably easier, as you will not have to deal with the danger of poisoned water while exploring. There is no longer a Stray Fairy underneath the water as there was in the N64 version, so this part is not as important as it once was, but it is still a wise idea to do so.