I think I would have liked the original plan better, with an ice rod and such. Still, this sounds very well planned out, and I'm looking forward to seeing the result.
Giving/Taking away the book based on what item you have selected sounds pretty doable, and easy to just throw into an existing quest without messing with the script too much.
I'd like to have ice magic, but it's something I can live without. I like the idea of just having two wands; two equipment slots, and have one wand disable the magic book when it is being used. That way, the "Sun Rod" works like a normal wand with the book, and the "Moon Rod" is a magic-firing non fire making wand item that disables the book (which Link will likely just have in his inventory from the start, invisibly). One other detail is the two wands would have different magic firing sprites (but I'm perfectly okay of this just being a palette swap), but I -think- you can do this in editor without scripting. I have to check again though since I haven't messed with the item editor in months.
EDIT: Hm, there is the triggering the two different wand triggers. One could be an FFC trigger that only works with that wand item ID, again, no real scripting expertise here 
Basically, one would be an item that is an actual wand and the other would just look like one (probably even have a different equipment slot) and through a fairly simple item script, interact with the portals you mentioned and harm enemies.
Overall, it sounds like you've thought everything through fairly well. (Probably better than I did whenever I tried to remake LTTP without scripts.) I might be interested in contributing some scripting to this, once you get things up and running.
Yeah, I think it could be an easy thing to script (but I really have no idea). There are a few scripts I'm willing to use but this won't be anything too crazy. It will still be a Classic styled quest at heart.
I appreciate the offer too, I will probably be looking for some scripting help, even if it is just having someone help me combine global scripts, if I can't figure it out. Most of the scripting for this project will be pre-made FFC scripts, and maybe two, or three globals, if they work together nicely. I need to get serious about building "The engine" of this project though. I have a lot of event based simple scripts that I had people make for me too, in the past, like one where you can step on a combo with an item to trigger secrets (three pendants-> warp to get Master Sword scene), and one where sounds play, and other little cosmetic/ "simple" stuff.
As a random note, there's actually a chinese bootleg called Triforce of God that is a straight-up 8-bit demake of ALttP. It's..... A bit buggy, and they shrunk down the dungeons, a lot.
Oh yeah, I actually found a ROM of that thing, and played some it it, and ripped some tiles from it. That project was my first 'attempt' at doing a NES demake, but the tiles are limited, and actually pretty ugly.That project became Link's Hangover, which can be found in my signature, if you are interested in seeing those tiles in action.
You don't seriously sketch on a chalkboard, do you? 
Lol, no, that's actually a sketch book page, that I scanned, and inverted the color on. I thought is looked easier to see, I guess 
It does look like a chalkboard, which might not be a bad idea.. that, or a dry-erase board. I do most of my drawings on printed "ZC graph" paper now though, that one is pretty old.
Which of the GB tiles are you using though? If it's for multi-tier dungeons, check out the Diagonal / First-Tier-Down tile packs by Lightwulf.
And if you need to go even deeper, I've been making my own Second-Tier-Down tiles as well, plus expansions to his originals for extra matching capacity/variety. I suppose I could pass some on, if those are the kind of tiles you're looking for.
Those are cool, but I don't think I'd be using diagonals. Mostly cause ZC lacks true diagonal collision, and also cause it feels kind of clunky with 8-way walking, sometimes. I will probably be designing most of the dungeons kind of like GB dungeons, which are basically smaller LttP dungeons.
I like this setup. Admittedly, I've grown used to slash over the last year, but I went without it for some 20 years before it ever made its way into my ZC games, so I have no problem going without it, especially if only for a while. Even if some people prefer it from the start, I agree that it would feel more rewarding to get it when you pick up the Master Sword. Consider some of the discussions people have had regarding multiple difficulty levels in quests: the most common opinion is that mere HP/Damage stat changes are the laziest method of implementation, while varying monster rosters/attack abilities/item techniques are the most thorough. Attaching things like the slash technique or Peril Scroll to the swords makes them a lot more worthwhile to obtain than just a sword that provides a mere damage stat increase.
Difficulty settings are a growing trend in ZC quests, but this quest probably won't have anything that complex. It will not be a challenge quest, but it won't be cake walk either. I like having one reasonable difficulty instead of dividing people between "hardcore" and "casual". You either get good enough to beat it as is, or quit. That's my philosophy. Not to say I wouldn't be opposed to having someone help me implement it in an update, if it is something that is wanted if this is finished, and popular enough. It's just not something I'm thinking about now for the project. tl; dr, I'm not doing it right away
