I've figured out a few more characters, so here's an update to the Zelda U Hylian alphabet cipher:
Figured out C, K, and M. J, Q, V, and X are the only ones left but I'm pretty sure I know what V is.
The towers dotted around Hyrule say SHEAKTOWER. Sheak = sheikah, obviously.
The tub that Link wakes up in at the start of the game. The only letters that weren't too blurry to read were NITCARE. I'm pretty sure it's repeating characters that probably spell out CARE UNIT.
CLOCK and THERMOMETER.
Update:
This gyroscope mechanism has GYROS written on it.
ROTATE
Previous translations:
The doors to every shrine have DUNGEON written across them repeatedly
The doors that seal Link inside the chamber he awakens in say SHUTOUT at the bottom. This word appears on other locked doors and gates throughout the world.
When Link puts the Sheikah Slate on a pedestal to gain a new rune it says
NOW LOADING
DO NOT TURN OFF
ALL YOUR BASE ARE
The area where the sheikah sits at the end of a shrine says GOALPOINT
The Hylian text below each named area on the map just says REGION
At the bottom is SHEAKERSTONE, which is probably engrish for Sheikah Stone.

Figured out C, K, and M. J, Q, V, and X are the only ones left but I'm pretty sure I know what V is.

The towers dotted around Hyrule say SHEAKTOWER. Sheak = sheikah, obviously.

The tub that Link wakes up in at the start of the game. The only letters that weren't too blurry to read were NITCARE. I'm pretty sure it's repeating characters that probably spell out CARE UNIT.

CLOCK and THERMOMETER.
Update:

This gyroscope mechanism has GYROS written on it.

ROTATE
Previous translations:

The doors to every shrine have DUNGEON written across them repeatedly

The doors that seal Link inside the chamber he awakens in say SHUTOUT at the bottom. This word appears on other locked doors and gates throughout the world.

When Link puts the Sheikah Slate on a pedestal to gain a new rune it says
NOW LOADING
DO NOT TURN OFF
ALL YOUR BASE ARE

The area where the sheikah sits at the end of a shrine says GOALPOINT

The Hylian text below each named area on the map just says REGION
At the bottom is SHEAKERSTONE, which is probably engrish for Sheikah Stone.