Great job on the sky box templates... only one problem. You're tackling this thing the wrong way. Think of how often anyone spends looking DIRECTLY UPWARD in Zelda... not very often. That being said, it is in everyone's best interests if you make the template in the following manner. (See PSD)
Reason being- it is MUCH more important that you tile the a seamless panoramic view across the horizon, than it is you make the most effective seam around the top of the box, because: you spend 90% of the game looking at the horizon, NOT directly upward, and into outter space. Don't get me wrong, having a perfectly seamless skybox is extremely important, because even the smallest seam can compeletely destroy the illusion, but we need to think of where the player's eyes will be focused during the majority of the game.
For comparison, you don't using the same sized texture on the face of a giant as you would for other characters. On the contrary, you make the textures of the feet/legs far more detailed. Why? Because the play is going to be looking at the giant's feet more often than the giant's face. Applying that same ideology to average scale characters, and you detail the face (larger texture) more than you detail the character's feet.
Of course, in this case it is important to have texture resolution be uniform across all tiles, simply to make editing easier, but the focus of the edit should be a seemless, and interesting horizon that generates depth. Not a seamless and interesting outterspace. We just don't look straight up in this game very frequently.
PS: You also don't have to rotate the tiles when saving them again utilizing this method.
