@Fishy: Yeah, I guess I was just trying to be overly comprehensive on that LA tunic bit.
Also, I think that might be true on Medigoron's Knife in
OoT--I'll have to take a look at it later.
At any rate, regarding the other issues that have been brought up:
- The Deku Stick upgrade at the Forest Stage (to my knowledge) can be obtained at any time.
- Regarding the Deku Nut upgrade, you can only obtain it with the Mask of Truth before pulling the Master Sword for the first time (you can meet the running man before this point, obviously). If you've already become an adult and try to return, the Deku Scrubs will do a variable amount of things (e.g. not appear at all, or appear and shoot you, etc.), but they'll never give you the upgrade.
- There are always enough Keys to get you through the Gerudo Training Ground and access the Ice Arrows.
- To obtain the Piece of Heart in
TP after the purple fog settles over that section of Faron Woods, just swing your Lantern--problem solved.