Bugs

This puzzle has lots of issues. Best give it a once over.
I've taken a look and see if I can make it better and hopefully it'll be good this time around.

This puzzle was also very confusing. Why can you push the mirror in the bottom right? The undercombo also looks odd.
Fixed.

After getting the lens, the secret here reset, trapping me.
I think I fixed it.

Cset error on the pillar.
Fixed.

There are several overworld locations where you can use the ladder to reach areas you're not supposed to. Keep the edges of land 2 blocks away from the screen boundaries to prevent this.
Fixed

This screen would be the only overworld screen that's completely empty and unreachable, except I reached it using the ladder bug I just mentioned. Why not put something here and complete your map?
How did I miss this Dx... Added something there so fixed.

Another example of the ladder problem. The north edge is too close to the top of the screen.
Fixed.

One more ladder problem. Even though it's a dock, you can still walk out onto it without rafting, then use your ladder to scroll to the right.
Fixed.

Pushing a block onto the switch in this room makes a secret noise, but nothing happens.
Fixed, Removed.

I bombed north in the room to the east of this one, went around, and then walked down into this room from behind the gleeok.
Fixed, Added a one way shutter on the other side to prevent this from happening.

And then I walked to the right and passed through this key door without having opened it.
Fixed.
-The Blue Ring doesn't change Link's color
Um... Link looks blue in the screenshots xD
-Splitting Darknuts are the same color as level 2 darknuts, making them impossible to tell apart.
Fixed.
-The left walls of your dungeons have two combos mixed up, resulting in an inconsistent pattern.
Well, thats odd I wonder why I didn't even see that. I may fix it... But dang going to do all them rooms are going to be tiring <_<
-Level 5's boss roar doesn't match the boss, and is in the wrong room.
Fixed.
-Several dungeons are on the same map. This is fine, but you should disable the space bar map in the dungeons so the player can't tell.
Fixed.
-Level 4's map isn't labeled.
Fixed.
-The boss key isn't visible on dungeon subscreens.
Added it.
-Level 4's triforce marker is in the wrong room on the minimap.
Fixed.
-There is no guy in the Wealth Medal room.
Fixed
-The scrolling pattern in the subscreen inventory is confusing, making it difficult to reach items on the lower row.
I'm not sure on how to fix that, I was able to get the item there and selctable but other then that I don't understand how that stuff works...
-There's no boss roar in the rooms surrounding Ganon.
Fixed
-After defeating Ganon, you can exit the room and return to fight him again. The doors remain open, though, so you can leave the room without beating him,
and his boss roar noise plays in every room you visit.
Added one way shutter to stop that from happening.
Questionable Design Choices

I accidentally released a ghost from a gravestone before defeating the rest of the enemies. Since the ghosts are undefeatable, and I had no key, this trapped me in the room.
I removed the graves, and replaced them with rocks.

I came here without the arrows and was trapped. There are a few dodongo rooms with a similar problem if you run out of bombs. I understand not being able to defeat these enemies, but getting trapped for it is pretty annoying.
Removed the shutter from the south entrance.

I'm pretty sure I found everything, but I had to cheat to reach the level 3 sword. I had already beaten the quest and got the level 4 sword first. I thought I tried every item to remove this beam, but could never find any way through. What did I miss?
You should be able to hit it with the wand itself (Not magic from wand.) and it should vanish. I tried it just now and it worked.