Quest for Truth:

After a revealing story sequence you'll be in the Deku Tree's meadow.  Leave Kokiri forest and if you have your horse, you can summon her with Epona's Song.  Now this next section tells how to get the Lens of Truth and the Mask of Truth.  You don't need to do this at this time, but since you CAN do it now, I thought I'd put it here.  If you don't want to do it yet, skip on to the section called Goron City Revisited.  First, if you don't have the Song of Storms yet, go to Kakariko and talk to the guy in the windmill and show him your Ocarina.  Now, head to Hyrule Castle and go into the Temple of Time's Master Sword room.  Sheik will be there and will teach you the Prelude of Light (very handy).  Now walk up to the pedestal and push A to return the Master Sword and warp back to being young Link.  Leave the Market.  At this time, the man running around Hyrule Field will finally appear.  Use him to complete Young Link's Trading Sequence (See section 3) and get the Mask of Truth.  Now go into Kakariko Village and enter the windmill.  Play the Song of Storms for
the music guy and the well will drain.  Climb down the well and walk into the passageway ahead of you and you're now in the Bottom of the Well level.

Bottom of the Well:

This level is nasty.  So, after 2 hours of mapping it out, I've found a way to get to the Lens of Truth very quickly.  There are a bunch of treasures scattered in this level but they are almost all WORTHLESS!  Most of them are a single Deku nut.  I'm going to tell you how to get the Lens of Truth, a gold rupee (worth 200 rupees), and finally the 3 gold skulltula's that are here (I've never mentioned most of the gold skulltulas before but explaining them here instead of making you explore this whole confusing level to get them is just easier.)  Crawl through the hole and climb down the ladder.  Kill the skulltula then walk straight forward right through the wall in front of you (yes, you heard right, this level has walls you can walk through, invisible floors, etc.).  Now you're in the main well room.  Watch out for the giant green flaming skull flying around and just keep running straight forward through another wall.  Now ignore everything in this room but watch out, there's a small invisible pit right in the center of the room where all that blood is.  Move around the pit and keep moving forward to the opposite wall and, again, walk through it.  Now stand on the Triforce symbol in front of you and play Zelda's Lullaby.  The water will drain out.

Now turn around and go back through the wall, avoid the pit, through the next wall, and you're back where you started, except now there's a big pit in front of you.  Fall down it and crawl through the hole that's down there.  Kill the skulltula, climb up the vines and go through the door to the Bottom of the Well boss.  This guy is scary but easy.  It's basically a swing-your-sword-wildly-at-anything-that-moves affair.