First off I gotta say I really love your arrangements! They're all really intuitive and well done! Your Riding (Day) for example is notated so well in comparison to another one I found online. And I love the way you notated the cuica in Goron City (Day)!
I was looking for a Lost Woods BotW arrangement, and yours was the one I found, so kudos! About the time signatures, I was going to suggest maybe adding a shifting time signature that changes every bar? This might destroy readability and your way of notating it might be the easiest on the eyes, and I know notating odd time signatures like this can go either way. But when I was listening through it along with you sheet music, I would say it feels like each D-G fourth interval (or second one if there's two in a row) emphasizes the start of a new measure.
For example, your first 10 measures, I would have written it out as:
Two measures of 3/8, one of 2/8, one of 5/8, one of 4/8, one of 5/8, one of 4/8.
Having it in my head this way helped me get the weird patterns down. I know this would probably mean redoing the sheet from the ground up, and your arrangement is great the way it is too, but just an idea, my two cents haha. Hope it's not out of line for me to suggest.