Lanayru Desert: when powering up the generators for the turn switch in the north desert to open the Mining Facility dungeon, two power up locations are visible on the map and look like mini temples, one is hidden beneath a bombable wall in of the seemingly dead ends in the...
Well, ok. One thing i see wrong is that when link was brought to Kokiri Forest, he was taken in by the Deku Tree to live among the Kokiri. so obviously they could have been there for who knows how long. and could never have come at the same time of links...
You remember in twilight princess when you go through the gate of time and find a hidden temple? The window that navi exits through is the same window that leads to the hidden temple in TP.
It's possible she lived out her life in there and never actually left the temple at all.
Did you set your arrows to Light Arrows on the item screen? When you go to the item screen, tap the arrow icon twice, and then the Light Arrow icon. If it still doesn't work, you're probably out of magic.
Also, this should be in the Zelda Game Help section.