-Do ending A first. I believe that's the intended order, that's what the manual directs, and if you progress and decipher your way through the game as it appears to intend, you would be unlikely to get ending B until it's your very last thing to do in the game, especially going for 100%.
Yes, you can continue your save after seeing ending A.
You do not need to do ending A to return to make things go back to how they were. If you'd like a hint how to do that, I recommend you check out the second page of the hints section in the manual. I think it's around page 20. You'll want to look at the notes and hints carefully and it may help if you're a bit tired.
This should also aid in going back to the other areas, but it may also help you to look closely at the pen and ink notations on certain pages, like the very well-hidden one on the warp spots page. Also, honestly I don't quite remember where these specific upgrades are but these hints should help generally send you in the right directions.
-You're really close on the fairies. Try doing that same sequence in one of the translated locations listed on the second fairy page. It's a spell to point you in the right direction in certain places. If you try it somewhere where there are no fairies, it will do something different than if you try it somewhere with fairies nearby. Those local truths will get you every time.
-Good catch on the Cathedral map! It may make a bit more sense when you can read the manual. Yep, you can decipher it using only hints from what you're given in the game. The second to last page of the manual gives the biggest hint to deciphering the language. It's very tricky IMO and took me and my spouse multiple days to figure out even with the hint. Between this part and the hidden puzzles in the game, a small
will be helpful.
-Being able to read the language will make the writing on the monument much clearer.
-If I'm thinking of the same chest, I think there's some kind of obscured path or bombable area to get towards it. I may have to get back to you on that.
-The windmill hint(s) are one of the hardest puzzles in the game, so give yourself more time, grace and puzzling experience there.
-Great catch on that save file. The notebook may come in handy for this part later, too.