You have three options here - left, right or up. Go right first - you'll probably fall into one of the many, many trapdoors in this dungeon. Mark them with your map. Back at the entrance, take the upper path and bomb a hole out of the wall. Back at the entrance, hit the right switch and follow your new bombed-out path to cross the bridge in time. Hit the floor switch up top, then do the same for the left side and move on down.
After acquiring the hammer on 3F (it's a pretty simple path), use it on the rusty switch. Then catapult yourself over the wall via the new "Step Right Up" tiles. Make your way back to B1, past the bone bridges and skele-pirate battle, on down to B2. Use your far-reaching hammer to hit all the switches and collect both a Courage Gem and key. Take said key back to the locked door on B1, lower the water level and move to the western portion of the map. Hit the triangle blocks in the center (don't stand on any!) to make them all turn into circles. This puzzle will appear later, only much more devious.
The catapult in the lower left corner takes you up high enough to hit another pyramid tablet with an arrow. The water will make the bone bridge rise. Solve the next circle and triangle puzzle to lower a nearby door. Head right of the new all-circles tile puzzle and up the bridge. Now that the door has been lowered, you have a clear arrow shot at the pyramid. Lower the water again and move down to B2.
Another tile puzzle. Make 'em all red, but know that you can hit outside of the grid to flip smaller chunks of the puzzle. It looks quite daunting but after a few big hits, you should just need a small series of surgical smashes to complete the puzzle. Return to B1 and look, it's yet another color puzzle. The first one you see is the "true form" that you'll have to replicate up top. Hammer your way up, use your boomerang to change the arrow-shooter's direction south and fire your own arrow into it. The water will rise and lead you to the puzzle. We suggest flipping the middle piece to its proper circle patter, then use smaller, more focused pounding around it. Remember: standing on pieces prevents them from flipping, and you can hit outside the grid to move two or even one piece at a time.
Lower the water and move to the now-opened door. Use the catapult to bounce the rock up high, then push it right to break the other boulder. Grab the key (and 100 rupees) and head to the locked door on the right side of B1. Soon enough you'll be staring at the Boss Key, which is a simple block ride away from this guy:
A very imaginative battle. Use the hammer to launch Link up to the Golem's chest and tap away with the hammer. You're aiming for its red joints. Run under his legs to get his back. Eventually he'll lose his body and come at you as a head - launch yourself on top and pound his blue weak point.
Before heading back to the blacksmith, use this time to explore the ocean and tie up any loose ends. There's a mermaid storyline on Bannan Island (detailed later in the guide), the various Travelers' Ships and Spirit Island too, where you can power up Link some more. When you're ready, Zauz will begin forging the new sword, but you'll have to face Jolene one last time before it'll be ready. Once you have the new sword, take it to Oshus and you'll be on your way to the end.