Wow! That's really comprehensive bug reporting, so thank you! I think you might be one of the first people to take a look under the hood of this ridiculous contraption by opening it up in ZQuest and looking at the FFC scripts, too, so that's helpful.
You would make an excellent betatester, by the way!
I checked out the Mickey Mouse mode problem:
So it's not as fatal a bug as I'd feared, but still really unintuitive and bad and dumb. Another thing I should try to fix if I can get version 1.4 done.
On certain screens, the ShovelSecret item and the room item/secret item seem to share the same flag
Ah, I was afraid there would be oversights about that. I'll try to get those fixed too. Good thing I put in extra seashell locations, I guess : /
In hindsight, this is precisely why most sane people probably use the Screen->D flags to keep track of unique item spawns, instead of setting Screen->State[ST_ITEM] and Screen->State[ST_SPECIALITEM] (or just don't cram multiple things on one screen quite so much). Alas.
another ShovelSecret I'm not sure about, in Marui at 4:69.
As far as I can tell, this one does work correctly. Marui does indeed have two secret seashells even though the others don't;. I think I thought the placement on this one was too obscure (I don't think most players would stop to think of shoveling under the crystals at that particular juncture). In hindsight, it probably should've been a P-Bag or something, but oh well.
As for the minor bugs...
Regarding the ungettable items...
For those curious about the prospects of 1.4 becoming extant, I haven't poked at ZC much lately, but I've been noting numerous problems from different LPs (and also that I need to put a more noticeable version number warning up, since this thing REALLY doesn't work right in anything but 2.50.2). I'm also still working on finishing some of the LPs (I can only stand to stare into the abyss of my own clunky game so much).
One of the biggest things I'd like to do, but that would involve a bunch of rescripting and restesting, is to essentially rewrite the awful spinner paths (or, failing that, just take a Parallel Remodel-esque hatchet to the 'challenge' of the spinner tracks so that people don't have to fiddle with it so much to get through the spinner rooms), but we'll see what happens.
I've also gotten a lot of complaints about the final boss having too much health (especially since he starts throwing a billion complications at you simultaneously by the end). Personally, I don't like it in a game when a final boss goes down easy without a long-winded beating that threatens to sap all my health, but, if I did another version it might be good to add some way to adjust his difficulty (speaking of taking ideas from Parallel Worlds).
Likewise, some people seemed to get hung up on how to use the ladder to get into the miniboss room (and up towards the boss area) in Yamauchi palace because they don't realize you're supposed to face upwards to use it to place it where you are, so, a little ladder rewriting (or an extra Impa hint telling you to face up when using it) might be in order. Not to mention some better Tower of Seline hints, and I'm tempted to try to add content to Zelda II Hyrule, and maybe make a real boss rush mode, and to set better default midis (and make them cooperate better with the script-changed music somehow), and...
...yeah. I pretty much just haven't dumped more time into this yet, but I'd still really like to fix it up at some point. Moreover, I'd like to make a whole new game and smply learn from my mistakes there, but responsibility demands spending a bit more of my time on things that will rude my odds of IRL doom thus far, so I've barely touched ZC in a few months, sadly. But someday, if I yet live and have the time to spare for it, then I'll do more with ZC.
Here's a look into deleted process, on that 'Northwest Calatia' thing I mentioned in one of the above spoiler blocks (regarding the ungetable secrets). These are three different prerelease updates of my scratch notes for when I was planning what items would go where.
Early on: (there were going to be 9 crystals in Calatia, one for each of the three 8x8 maps)
(the red bottle became the Habanero Pepper; it was going to be Hot Sauce instead. Din's Fire was just Din's Fire, the Horse Call was the Pegasus Boots, the Life Spell was the heart-shaped Life Wand, Zelda was going to get her own version of the vanilla ZC fast-shooting longbow item, and the Lens of Truth was going to be in the quest. At this point, I wasn't intending to use ZII Hyrule, so the Tower of Seline in the Northwest, with the magic key in it, would've been the final dungeon. The boss list talking about 'Urchins' meant 'Unira', I hadn't looked up the proper name for the Clu Clu Land enemies yet when I made these notes.)
Later: (By this point I had thought about 12 crystals in Calatia, but I had decided to axe the third 8x8 map due to lacking ideas. I left the notes for it intact anyway.)
Closer to release, after getting some betatester feedback:
As you can see, there's some differences that made it pretty far in the game. I'm not sure why I left a note for 'Peril' in the southwest when I'd long since put the Peril Beam scroll in-game in the southeast (and had no intention of using Peril Rings since I'd already used them for the level-up system and guardian acorns), but that just shows how disorganized my notes were.
At one point during testing, Dimentio spontaneously designed a would-be Northwest Calatia area, but due to complications in how he set it up and due to finishing it being more than I wanted to chew, and due more generally to the fact that I'd designed the quest solo otherwise and wasn't sure about how best to work with his contributions, I didn't wind up using his map. But it was pretty cool-looking and I hope he puts it to use in some other way at some point, since as I've said before, this quest is open source and people can use stuff from it as they like (if they can figure out how to do so).