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, there are two ways to hit it without the timeshift stone.
By standing in a specific spot next to the gate blocking the puzzle blocks, you can shoot behind the grating covering the eye and hit it. This shot is extremely precise, but saves about 3 seconds over running to the lower level.
After entering the area, run down to the lower level, stand underneath the target, and shoot upwards. This shot is easier than the above but slightly slower.
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.
Whatever method is used, these shots skip having to use the Gust Bellows and 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. The only difference between the two is that Dreadfuse is shinier and left-handed.
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.
The fastest way to kill the Zombie Bokoblins that spawn is to fight the Stalmaster normally until they close in, then plant a bomb and slash it with your sword, killing the bokoblins while damaging yourself.
A slightly safer and slower method is to place a bomb at the very start of the fight without moving. When the Stalmaster begins to attack, shield bash if necessary and back away, letting 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.
It's possible in the Cistern Basement room to knock the Iron Moblins into the void by grabbing onto the edge of the platform and boosting into them.
The trick is inconsistent and difficult, so this would be considered segmented or TAS only.