By using the appropriate routing, you can skip the Earth Temple room in Sky Keep. The current route has four different instances where you shift blocks in the puzzle; the puzzle solutions and a brief route outline are below.
For the puzzle directions below, the direction indicates which block you should move into the blank spot. So R means take the block to the left of the empty spot and move it to the right.
This puzzle takes 16 moves, as follows:
Once the rooms have shifted, proceed through the door. Clear the Skyview Temple room and make your way through the Lanayru Mining Facility Room to the control panel there.
This puzzle takes 2 moves, as follows:
Once the room has shifted, proceed through the same door that you entered the room. Back track through the Skyview Temple room and enter the Fire Sanctuary room. Grab the Triforce of Power and exit back to the Entrance room.
This puzzle takes 12 moves, as follows:
Once the room has shifted, proceed through the door and get the Triforce of Wisdom from the Sandship room. Return to the Entrance room.
This puzzle takes 7 moves, as follows:
Once the room has shifted, run through the Skyview Room to Dreadfuse's room. Defeat him for the small key, and run through to the Cistern Room to get the Triforce of Courage.
In the first room, you can skip using the Beetle to knock the rope loose by using a precise bow shot.
You can also skip the first rotating vine drum by standing in a specific spot and shooting the Clawshots directly to the second rotating vine drum.
In the LMF Room, it is possible to hit all six eye targets behind their grating without using the timeshift orb. For the first target, run down to the lower level, stand underneath the target, and shoot upwards. For the next five targets, by standing in specific locations and shooting at a precise angle, you can hit the eyes' hitboxes before the arrow hits the grating.
This skips having to use the Gust Bellows and skips bringing the timeshift orb with you through most of the room.
When you enter the Fire Sanctuary room containing the Triforce of Power, clip though the vine in front of you with Clawshot Vineclip. You will land OoB; run over to the other side of the room and use the clawshot on the vines next to the Triforce symbol to get back inbound.
It is possible to hit the first bow switch while standing on the dirt patch located in the center of the room.
The strategies for Dreadfuse are exactly the same as those for Scervo in the Sandship; see that page for details.
Because Stalmaster operates on a one hit = one damage principle, the strategies here are the same as the strategy for the Stalmaster in Ancient Cistern; see that page for details.
At the beginning of the fight, place a bomb at the Stalmaster's feet without moving. When it begins to attack, back away and let the Zombie Bokoblins converge on the bomb; it should explode, killing all the Bokoblins and stunning the Stalmaster. You can then finish phase one in two rounds as usual.