Wow, many questions! Let's get at them......
ms_zelda_lady:
You can burn the big limestone block at north, going south from there eventually takes you to the south middle key. You can bomb a ruined eyeball statue at the northwest, this takes you to the east ledge key.
Lithium:
First I thought it was a bug, then Twilight_Knight's post reminded me of the Secret Deluxe ending. You are the first who found that, and with it, being nitpicky, we could say that you were the first to beat BB...

TheOnlyOne:
You are a great player rushing to fabled Garden Gallery and asking for help only there. So...
If you don't know where's the warp to the miniboss corridor, then how do you know that it exists and that you get to shoot a bug after it and that it earns you the boss key and that it immediately lets you onto the boss? ???
Also, there are two blue crystals at the southwest of the big circle room of F1. Shoot both of them with your nice new arrow.
The secrets/triggers are indeed obscure, but I like it better than if you already knew what to use upon entering the room. Or I just simply can't make the alternate between too obvious and too obscure.

At the later items, when you get them, you get some tips on how can you use them, I wonder if it suffices then... *Imagines TheOnlyOne with a completed inventory, frustratedly trying to blow a hammer, whacking a door with a medal, shooting a bracelet from a crossbow and yelling "I ALREADY TRIED EVERYTHING!!!!!" *
Zenith:
Yes, bombs are good to destroying machines, like spike mechanisms...

Zorlaf:
How did you learn that there is an Ocarina of Blood? Twilight_Knight pointed you in the good direction, but I don't think you are at Mt.Dead End yet...
judasrising:
Twilight_Knight said it well.
EDIT:
Zorlaf, you can't get that chest, it's just for fun!

"running chest", nice name.