Final update (unless there is a game-breaking bug):
Hero Mode 1st & 2nd Quest
All 3-stair warps are enabled in both Hyrule and Lorule. One screen away from each of the 3-stair warps (up to you to find), there is a whistle warp that leads to the respective other world. There are also three additional warps between Hyrule and Lorule (whistle to reveal warp spot) for easier traveling at locations that are further away from the usual warp spots. With the recently introduced new raft paths in both overworlds and the fixed Level 8 whistle whirlwind warp spot in the 2nd HM quest, mobility is as good as it can possibly get, and it should hopefully not be an issue at all anymore.
Also, you can now continue from the Lorule starting screen even after having saved. This is particularly helpful once you have beaten all five Hyrule dungeons and you usually have no more need to go back to Hyrule except maybe for a missed arrow or / and bomb upgrade.
Lost Levels 1st, 2nd & 3rd Quest
All whistle whirlwind warps are enabled now, the whistle whirlwind no longer brings you back to the starting screen of the Minirule overworld (DMap setting adjusted). You can now warp to the entrances of Levels 1 through 8 if you have claimed the respective Triforce piece.
Crazy Challenge
All 3-stair warps are enabled in both Hyrule and Lorule. Since there is a permanently active Hyrule-Lorule warp right at the starting screen of each world, the whistle warp next to the normal 3-stair warp is not available. However, there are three additional warps between Hyrule and Lorule (whistle to reveal warp spot) for easier traveling at locations that are further away from the usual warp spots. Mazes have been taken off this quest already in the past, so mobility is very high already.
Also, you can now continue from the Lorule starting screen even after having saved, even though there is a warp right at the starting screen. Some players want to run off right away. 
Ultimate Challenge
There is a new whistle whirlwind warp ring active that covers the original NES LOZ 1st Quest entrances of Levels 1 through 8 (which are also the entrances of Levels 1-1 through 8-1 in the UC). Due to limitations of the whistle item (only one warp ring for one whistle), that is the best I can do for you guys. Mazes have been taken off this quest already in the past, so mobility is very high already.
Also, you can now continue from the Lorule starting screen even after having saved, even though there is a warp right at the starting screen. Some players want to run off right away. 
The final update is now live. Feel free to download them by the following links:
The Legend of Zelda - Hero Mode - Quests | PureZC
The Legend of Zelda - Lost Levels - Quests | PureZC
The Legend of Zelda - Challenges - Quests | PureZC
Edit: Hotfix for Hero Mode (missing guy in Lorule desert cave of 1st Quest) now live. Sorry. 
Edited by Matthew Bluefox, 26 April 2025 - 11:03 AM.