Just played through the newest version and it's pretty damned flawless.
Only real thoughts I had (which you probably already thought of) are:
I wonder if there might be a way to add a couple rooms in dungeons or replace rooms with relatively worthless hints and add a couple places where you could buy increases to your arrow capacity, like the bomb upgrades. Like you start with 30 and maybe one spot to increase your capacity to 50 and a second to increase it to 70, and then when you get the silver arrows it bumps you up to 99.
Another little idea I had today, that might be impossible to implement, but just throwing it out there: I wonder if there'd be a way to add a second upgrade to the shield that makes the big shield not just block, but reflect the projectiles back at the enemies, like in some of the later games?
And then just a personal annoyance with the original game: I wish there was a way to turn off the magic book's effect on the Magic Rod, so it doesn't always produce fire when the beam hits. Too often, I end out smacking into residual fire that it leaves behind. I know I could always just not get the book in Level 8, but I just wish it was an effect you could turn on and off. Again, that's not a flaw you introduced to the game, it's just an annoyance that's always been there.
Anyway, amazing, near-perfect work so far. Can't wait to see what other surprises you have in store once you have the mapper hack worked out.