Wow! Thanks a lot for positive feedback.
I'll admit I encountered some of the same problems that you mentioned while making the dungeon: Having to swap tools, forgetting them in various places, and those were some of the reasons why I added empty pedestals in the living quarters and added the pouch in one of the chests.
I made each area with the thought that you would either be able to clear it with nothing but boomerang, or need to find an item from somewhere else first, for example sailcloth before feather or grapplehook before Hermes boots. I actually had to swap the location of a few items before first upload, because I noticed I was trying to give the same item twice in different locations, and I also had to keep tool limitations in mind.
I wonder how that color switch status was blocking the way. Did you use a teleport to get out of the pool to the hub area? If you unlocked the teleport in the first room in the pool then you should have been able to use it to go back. The first room in the pool should only have color switches that require manual actions from the player so I'm not sure how you'd be able to get out there while doorway is blocked aside from using the teleport, and there shouldn't be contraptions that would change it when entering the room. I'm glad to hear that you were able to use bomb-vases as a replacement.
Are you able to describe the place for "grappleshot north for the blue gem" more closely? Just in case if I'm thinking about wrong place.
Honestly speaking I didn't bother to fully test the dungeon with every possible number of combinations for what actions a player might take. I tried my best to provide necessary tools and resources in order to avoid softlocks. You are right that the skeleton key is likely unnecessary, but I suppose I wanted to provide it just in case the player would miss most of the other keys.
I'm glad you had fun and enjoyed the dungeon, and were able to complete it.