Ah, I see that I should have read the change log more carefully.
Thanks for being very responsive!
There seems to be a new graphical bug. Some objects appear to have a lot of banding.
Grass (not the best demonstration, but there is significant banding on the grass in-game)
The game sometimes wouldn't load when I selected it in the menu. I wasn't able to load my save at all.
The exit button in the menu also didn't work for me; I had to alt+F4 to exit each time.
EDIT: I'm not sure if this is a driver issue since I recently updated them.
I've run into a bit of a problem. I cannot separate the background and the walls/floor of the second palace.
This means that Link must exist either in front of both the background and the ground he stands on, or behind both. Neither is pleasing.
I wish I had screen shots to demonstrate the problem, but I (stupidly) forgot to take them and I'm not ready to spend ~2 hours to get back to that point (for now, at least).
Look at this picture from the original. Now imagine that the background was (instead of bricks) a bunch of chains whose width scales the entire z-axis (from behind the red blocks to in front of Link).
Is this a bug with 3DNes or some unfortunate effect of the way Zelda II was programmed?
Unfortunately I don't think I'm skilled enough at Zelda II to get all the way through the game.
To be honest, I can't even beat the game with saving progress and a friend to help.
I might be able to set aside some time this week to reach beyond where I left off last time but I don't think I could ever reach the end in one run.
For some reason I couldn't get your .3dn working so I made my own.
EDIT: I worked some more on the .3dn.
EDIT2: I worked on the .3dn just a little more.
(Remember to rename the download to the name of the .nes file)
Let me know if you recommend any changes.